26th October 2017 – Learning Topic 2

26th October 2017 – Learning Topic 2: Pedigree Drawing
It was useful to revise the topic on Pedigree Drawing although I have knowledge on Pedigree Drawing from my previous studies, it was a useful refresher.
Pedigree Drawing is a drawing of a family tree which is used to identify and assess indications and patterns of families which would help in both diagnosing and managing the health of individuals as the pedigree drawing gives a depth insight of past health history.
I had found the lecture topic of Mendelian Inheritance interesting as this was an area where my knowledge was limited. As a biomedical scientist, it is important to keep updated with new techniques and knowledge because as biomedical scientist you are continuously developing knowledge and new skills throughout your career. This topic was beneficial as this is something that would be encountered daily by a biomedical scientist as certain disease are inherited.
Briefly describe Mendelins Inheritance Laws.
There are three main “Laws” of inheritance, which are, the law of dominance, the law of segregation and the law of independent assortment. Below are the three laws which are listed and briefly described.
The law of dominance is where some alleles are dominant whereas the other are recessive; the effect of the dominant allele will display an organism with at least one dominant allele.
The law of segregation the second inheritance law occurs during gamete formation, this is where the alleles for each gene segregate from each other so that each gamete carries only one allele for each gene.
Law of independent assortment is where the genes for various traits segregate independently during the formation of gametes.

References
High-throughput pedigree drawing
Ville-Petteri Mäkinen, Maija Parkkonen, Maija Wessman, Per-Henrik Groop, Timo Kanninen & Kimmo KaskiEuropean Journal of Human Genetics (2005) 13, 987–989. doi: 10.1038/sj.ejhg.5201430;
published online 4 May 2005. Available at https://www.nature.com/articles/5201430. Accessed on 26th October 2017.

With reference to the above article, it states how family trees have been used as a valuable visual tool for geneticists in identifying clusters of inherited traits and genotypes. Within this article it looks at the importance of family tress and how they help in inherited traits and genotypes, in addition to this the article looks at how pedigree drawings should be drawn. After reading this article I found it was interesting but when coming to an overall judgement on whether this subject has made a huge impact, I believe the article was not in much depth for me to reach a decision.

Multipoint Quantitative-Trait Linkage Analysis in General Pedigrees. Laura Almasy and John Blangero Volume 62, Issue 5, May 1998, Pages 1198-1211. Available at https://ac.els-cdn.com/S0002929707615420/1-s2.0-S0002929707615420-main.pdf?_tid=96fb6f44-ef31-11e7-8d7c-00000aab0f6c&acdnat=1514838372_9a544c524c7ca24c195b65f869947a9f. Accessed on 26th October 2017.
The above article discusses the multipoint linkage analysis of quantitative-trait loci. The article stated how variance-component linkage methods are used in pedigrees of arbitrary size and the complexity but also it looks at how they have developed general framework for multipoint identity-by-descent probability calculations. When reading further into the article different methods are investigated, methods like Variance-Component Linkage Analysis in General Pedigree, Estimation of the IBD Probability Matrix for a Genetic Marker, Derivation of IBD Correlation Formulas for Multipoint Analysis, each of the methods are discussed in depth within the article where a description is provided. I personally believe that after reading this article that this subject has made an impact as this article goes in depth as each method is discussed separately.
Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, et al. Completing the map of human genetic variation, Nature, 2007, vol. 447 (pg. 161-165). Available at https:// https://www.scopus.com/record/display.uri?eid=2-s2.0-0025172940&origin=inward&txGid=661088e35c2e782eda7de11696e6586f. Accessed on 26th October 2017.
With the article above, I had found that this article discussed how long-scale studies of human genetic variation have focused largely on the pattern and nature of single-nucleotide difference within the human genome. I personally believe that after reading this article that this subject has made an impact as this article goes in depth.

Modeling genetic inheritance of copy number variations. Kai Wang, MahletG. Tadesse, Joseph Glessner, Struan F. A. Grant, Hakon Hakonarson, Maja Bucan, Mingyao Li. Nucleic Acids Research, Volume 36, Issue 21, 1st December 2008, pages e138. Available at: https://academic.oup.com/nar/article/36/21/e138/2409932 Accessed on 26th October 2017.

The art of pedigree drawing: algorithmic aspects. Frédéric Tores, Emmanuel Barillot Bioinformatics, Volume 17, Issue 2, 1 February 2001, Pages 174–179. Available at https://doi.org/10.1093/bioinformatics/17.2.174 26th October 2017.

27th October 2017 – Learning Topic 3: Risk Assessment
Revising the topic on Risk Assessment was useful to revise as although I already possessed knowledge on Risk Assessment it was helpful to use as a refresher as this was a topic which was studied in my previous studying.
It was beneficial to study the topic on Angelman Syndrome, imprinting and risk assessment but however I preferred studying Angelman Syndrome as this is where I lacked knowledge. CPD is an essential element for a Biomedical Scientist to understand and after studying this learning topic I have gained knowledge on an area where my knowledge was limited.
I had read the provided research paper upon Principles of Genetic Risk Assessment which was intriguing to read as the paper provided me with knowledge. It is important for me as a Biomedical Scientist to understand CPD as this is a major part in involving within my career, after reading this I had developed a broader understanding, as well as at the same time developing as a biomedical scientist.
Define Angelman Syndrome?
Angelman Syndrome is known to be a rare neuro-genetic disorder which primarily affects the nervous system which is characterized by severe mental retardation. The causation of Angelman Syndrome is the deletion of the maternally inherited UBE3A gene which is located within chromosome 15q11-q13. The UBE3A gene is encoded at 100kDA protein which functions as Ubiquitin Ligase and Transcriptional Coactivator. There are a range of symptoms of Angelman Syndrome, symptoms include;
• Development Delay
• Speech Impairment
• Balance or Movement Disorder
• Behavioral Uniqueness
• Delayed and Disproportionate Growth in head circumference
• Seizures
• Hypopigmented skin and eyes
• Tongue suck and swallowing
• Strabismus
• Hyperactive Tendon Reflexes
• Feeding problems in infancy
• Prominent Mandible
• Increased sensitivity to heat
• Wide-spaced teeth
• Sleeping Disorder
• Frequent Drooling
• Smooth Palms
• Excessive chewing and mouthing behaviors
References
Heshka JT, Palleschi C, Howley H, Wilson B, Wells PS. A systematic review of perceived risks, psychological and behavioral impacts of genetic testing. Genet Med 2008; volume 10, pages19-32. Available at http://cel.webofknowledge.com/InboundService.do?customersID=atyponcel&smartRedirect=yes&mode=FullRecord&IsProductCode=Yes&product=CEL&Init=Yes&Func=Frame&action=retrieve&SrcApp=literatum&SrcAuth=atyponcel&SID=F3yWfx69M9DvwnJAlIc&UT=WOS%3A000252542700004. Accessed on 27th October 2017
After reading the above article referenced, it describes genetic testing and how it helps in the early detection of disease as well as looking at how effective the strategies of prevention are. The article begins to develop on how genetic risk helps look at behavioural change but however the impact of the carrier status from the viewpoints of psychological, behaviour and perceived risk perspectives are not fully understood. The paper further looks at literature review which is performed to identify studies which measured the perceived risk, psychological, behavioural impacts of genetic testing on individuals. The studies which were investigated were not limited to certain disease, but they excluded the impacts of testing for single gene disorders, further studies looked at hereditary nonpolyposis colorectal carcinoma, hereditary breast and ovarian cancer and Alzheimer disease. When coming to an overall judgement, I had found that this paper was rather intriguing as it was written in depth which helped not only gain knowledge but made it interesting.

Principles in genetic risk assessment
Pedro Viana Baptista
Author information ? Copyright and License information ? Disclaimer https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1661604/

The above article states how a risk assessment constitutes an essential component of genetic counselling and testing, it has been said in the article that the genetic risk should be estimated as accurately as one can for an individual and family decision making. The article also described how all relevant information which was gathered from the population studies, pedigrees and genetic testing enhances the accuracy of the assessment of a person’s genetic risk but also it emphasised how this review would focus on the general aspects implicated within the risk assessment; the increasing genetic information regarding disease; complex traits versus Mendelian disorders; and the influence of the environment and disease susceptibility are factors which would be provided. The influence of the factors were provided and discussed within the article.

Down Syndrome: Prenatal Risk Assessment and Diagnosis
DAVID S. NEWBERGER, M.D., State University of New York at Buffalo, Buffalo, New York
Am Fam Physician. 2000 Aug 15;62(4):825-832 https://www.aafp.org/afp/2000/0815/p825.html

With reference to the above article I had found that Down Syndrome (Trisomy 21) was the most commonly recognized causation of mental retardations. Trisomy 21 is the risk which is directly related to maternal age, however all the forms of prenatal testing for Down Syndrome must be done voluntary. The article described how a nondirective approach should be used when patients are presented with various options for diagnostic testing and prenatal screening. The patients which are 35 years of age or older are offered chorionic villus sampling or a second-trimester amniocentesis on their due date, females who however or younger than 35 years of ages would be offered a maternal serum screening at 16 to 18 weeks of gestation. Alpha-fetoprotein, unconjugated estriol and human chorionic gonadotropin are maternal serum markers which are used to screen for Trisomy 21. The article stated how the use of an ultrasound to estimate gestational age helped improve the sensitivity and specificity of the maternal serum screening.
In reference to the article, after reading the article referenced I had found that Down Syndrome is a variable combination of congenital malformations which were caused by trisomy 21. This is known to be the most commonly recognized genetic causes of mental retardation and is approximated prevalence of 9.2 cases per 10,000 live births in the US, the article looks at the cases of Down Syndrome within the US.

Genetic Risks to the Mother and the Infant: Assessment, Counselling, and Management
Stuart K. Shapira1 and Siobhan Dolan https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592163/

Genetic Risk Assessment for Adult Children of People With Alzheimer’s Disease: The Risk Evaluation and Education for Alzheimer’s Disease (REVEAL) Study
J. Scott Roberts, PhD
, L. Adrienne Cupples, PhD
, Norman R. Relkin, MD, PhD http://journals.sagepub.com/doi/abs/10.1177/0891988705281883 First Published December 1, 2005

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28th October 2017 – Learning Topic 4: Dysmorphology
Dysmorphology was the other learning topic which I had studied, again due to my previous studying I had a vague idea of Dysmorphology, but it was useful to study this again.
The lecture topic on this area (Dysmorphology) was interesting as this topic led to discussions which had opened this lecture topic further. Dysmorphology was a lecture topic regarding the developmental structural defects, this was a refresher for me as this was studied previously. I had found this learning topic fascinating as it had covered a variety of elements which opened discussions but also in-depth theory which was provided had made it interesting as I was able to absorb more knowledge. The paper on Dysmorphology and Jouberts Syndrome was rather interesting to read as it has provided information on key areas which would help later.
There are two key factors which a Biomedical Scientist like one must consider throughout their career, development on knowledge and skills are the two major factors which would help me develop and prosper within my working field.
It is equally important for me as a Biomedical Scientist to keep updated with the new techniques and knowledge as development of techniques and knowledge is a cyclical cycle as a Biomedical Scientist is continuously developing knowledge and various new skills.
Portray a portion of the terms which are routinely used in birth defects.
• Malformation or Anomaly are a primary defect which is caused by the basic alterations in the structure, this occurs before ten weeks of gestation. Cleft Palate, Anencephaly, Agenesis of limb or part limb are examples of Malformation or Anomaly birth defects.

• Malformation Sequence is the defect pattern of numerous defects which result from a single malformation. Talipes is a key example of malformation sequence also referred to as Clubfoot and Hydrocephalus can result from a Lumbar Neural Tube Defect.

• Malformation Syndrome defect is a pattern of features that often have an underlying cause, these commonly arise from several different causes in Morphogenesis. This consists of Chromosomal Disorders such as Down Syndrome, Microdeletion Syndromes like Prader-Willi Syndrome, Polygenic Disorders as well as Club Foot, Environmental Causes (Teratogenesis) such as Rubella, Congenital Viral Infection.

References

Chapter 7 – Next Generation Sequencing in Dysmorphology Robert Smigiel1, Urszula Demkow2 2016, Pages 137–151 available at https://www.sciencedirect.com/science/article/pii/B9780128017395000076. Accessed on 28th October 2017

In regard to the article referenced above, it highlights the dynamic progress in molecular techniques which have created new diagnostic tools in dysmorphology. The article begins to examine how some dysmorphic conditions can be recognized by detailed clinical examination which are accompanied by convectional karyotyping, multiplex ligation-dependent probe amplification tests and array comparative genomic hybridization (aCGH) analysis. The article begins to develop on Sanger Sequencing which is of single gene which exclude genomic imbalance and point mutations as well as next generation sequencing which have helped in the rapid identification of known heterogenous entities and novel genetic syndromes. Again, when judging the above article, I had found it interesting to read as the level of depth which was provided showed that this subject had an impact as this article looked at the various molecular techniques in Dysmorphology.

Down syndrome—recent progress and future prospects
Frances K. Wiseman, Kate A. Alford, Victor L.J. Tybulewicz, Elizabeth M.C. Fisher
Human Molecular Genetics, Volume 18, Issue R1, 15 April 2009, Pages R75–R83, available at https://doi.org/10.1093/hmg/ddp010. Accessed on 28th October 2017

The above article looks at Down Syndrome and the causation of this disease. Down syndrome is known to be caused by trisomy of chromosome 21 which is associated with various deleterious phenotypes which cause learning difficulties, heart defects, early-onset Alzheimer’s disease and childhood leukemia. The article examines recent research undertaken on Down Syndrome which looks how patients and relevant animal models, the article refers to the advances in therapy used to improve cognitive function in individuals with Down Syndrome as well as the significant developments in understanding the trisomy of chromosome 21 gene. In addition to this the article it investigates future research directions considering new technologies, the use of chromosome engineering to generate new trismic mouse models. The paper overall regarding Down Syndrome was written in depth but however I still personally believe that this has not particularly made an impact on this certain topic yet more research needs to be done.

The prevalence of Down syndrome in County Galway. O’Nualláin S , Flanagan O ,
Raffat I , Avalos G , Dineen B. Irish Medical Journal 01 Jan 2007, 100(1):329-331 available at http://europepmc.org/abstract/med/17380922 Accessed on 28th October 2017
The referenced article above looks at the retrospective survey of all cases of Down Syndrome which were recorded between 1981 and 2000 mothers who were resident in Co. Galway. The article looks at studies and makes a comparison of the incidence of Down Syndrome in both decades which then examines the effects of changing demographics on incidence rates. The paper further looks at the overall prevalence rate in the previous decade. It was founded that Down Syndrome was significantly increased in women whom are over the age of 30. I had found the paper was interesting to read as it showed how over the decades the number increased but also the paper looked at how Down Syndrome linked but I believe that this article has made an impact.

Dysmorphology demystified William Reardon and Dian Donnai Arch Dis Child Fetal Neonatal Ed. 2007 May; 92(3): F225–F229. Available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675338/ Accessed on 28th October 2017

Is Down syndrome a disappearing birth defect? Collins VR, Muggli EE, Riley M, Palma S, Halliday JL
The Journal of pediatrics 2008 Jan;152(1):20-4, 24.e1 Available at http://europepmc.org/abstract/MED/18154892 / Accessed on 28th October 2017

29th October 2017 – Learning Topic 5: Chromosome Analysis
It was useful to revise the topic Chromosome Analysis. Even though I have knowledge on Chromosome Analysis it was a useful refresher. I have studied this area in my previous studying.
I found the lecture topic Chromosome Analysis quite interesting as this was an area which is discussed a lot. Chromosome Analysis is the process which evaluates the number and structure of an individual’s chromosomes to detect abnormalities, this was studied during my previous studies which meant that I had knowledge on this area already but by studying it again it enabled me to refresh my mind and develop a better understanding of chromosome analysis. Cytogenetics was a topic which was discussed in depth making it interesting.
Having the role of a biomedical scientist, understanding new techniques is important as this would help me tackle everyday situations in a new way, but as well as this as it is important for myself to ensure I have new knowledge which can be brought forward into my work to help me develop better and accurate results.
As a biomedical scientist it’s important to keep update with new techniques and knowledge, because as a biomedical scientist you are continuously developing knowledge and new skills throughout your career.
Provide an explanation of your understanding of the term “Karyotype Analysis” providing examples of diseases which can be detected by a Karyotype.
Karyotype analysis is the process which is used for the identification of abnormalities within chromosomes, this includes missing chromosomes, extra chromosomes, deletions, duplications and translocations. These specific abnormalities can cause genetic disorders like Down Syndrome Turner Syndrome, Klinefelter Syndrome and Fragile X-syndrome, below are examples of abnormalities identified by Karyotype analysis;
? Down Syndrome (Trisomy 21): This is where one has an extra copy or third chromosome 21 which then causes learning disabilities as well as the physical characteristics of an individual.
? Edwards Syndrome (Trisomy 18): This is where a person has an extra 18th chromosome.
? Patau Syndrome (Trisomy 13): This is where an individual has extra 13th chromosome but however one would not survive more than a year as they would usually have cardiac problems and severe mental impairment.
? Klinefelter Syndrome: Klinefelter Syndrome is when a male has an extra X chromosome (XXY).

References
Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome.
Goidts V1, Cooper DN, Armengol L, Schempp W, Conroy J, Estivill X, Nowak N, Hameister H, Kehrer-Sawatzki H. https://www.ncbi.nlm.nih.gov/pubmed/16838144?dopt=Abstract

With regards to the above article, it was founded that structural diversity of the human genome was much higher than previously assumed although the full extent remains unknown. The article had stated that to investigate the connection between segmental duplications which display constitutive copy number difference between humans and the great apes and those which exhibit polymorphic copy number variations between humans, it was analysed a BAC array enriched with segmental duplications which displayed such CNDS. The study documents for the first time in addition to human-specific gains common to all humans, these duplications clusters (DCs) also exhibit polymorphic CNV ; 40kb.

Science. 2002 Aug 9;297(5583):1003-7.
Recent segmental duplications in the human genome.
Bailey JA1, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. https://www.ncbi.nlm.nih.gov/pubmed/12169732?dopt=Abstract

With reference to the article it had looked at how primate-specific segmental duplications were considered significant in human disease and evolution. The inability to differentiate between allelic and duplication sequence overlap had hampered the characterisation as well as assembly and annotation of our genome. The article further explained how a developed method whereby each public sequence was analysed at clone level for overrepresentation within a whole-genome shotgun sequence. The test had the capability of detecting duplications which were larger than 15 kilobases irrespective of copy number, location or high sequence similarity. The article described how the researchers mapped 169 large regions flanked by highly similar duplications, 24 of the hot spots of genomic instability had been associated with genetic disease. The analysis had indicated a highly non-random chromosomal and genic distribution of recent segmental duplications with likely roles in expanding protein diversity.

Nat Genet. 2006 Jan;38(1):82-5. Epub 2005 Dec 4.
Common deletions and SNPs are in linkage disequilibrium in the human genome.
Hinds DA1, Kloek AP, Jen M, Chen X, Frazer KA. https://www.ncbi.nlm.nih.gov/pubmed/16327809?dopt=Abstract

Regarding the article referenced, after thoroughly reading this article it was founded that humans show a great variation in phenotypic traits such as age, height, susceptibility to disease and eye colour. The genomic DNA sequence differentiates between individuals which are responsible for the inherited components of these complex traits. The article had showed that reports suggested that intermediate and large-scale DNA copy number and structural variations were prevalent enough to be a vital important source of genetic variation between people. Due to the association studies to identify genomic loci associated with particular phenotypic traits had focused primarily on genotyping SNPs, it is important to determine whether a common structural polymorphism are in linkage disequilibrium with common SNPs and which can be assessed indirectly in SNP-based studies. The article had presented a test which examined 100 deletion polymorphisms ranging from 70 bp to 7kb. It was showed that common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs which indicated that polymorphisms may share evolutionary history and that most deletion polymorphisms were effectively assayed by proxy in SNP-based association studies.
PLoS Genet. 2006 Feb;2(2):e20. Epub 2006 Feb 17.
Bias of selection on human copy-number variants.
Nguyen DQ1, Webber C, Ponting CP. https://www.ncbi.nlm.nih.gov/pubmed/16482228?dopt=Abstract

Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE (2005) Segmental duplications and copy number variation in the human genome. Am J Hum Genet 77:78-88 https://www.ncbi.nlm.nih.gov/pubmed/15918152?dopt=Abstract

30th October 2017 – Learning Topic 6: Biochemical Diagnosis
The topic Biochemical Diagnosis for me was the second most difficulty one to understand at the start, however after studying all the lectures a couple of times I started to grasp the understanding of Biochemical Diagnosis.
After studying the lectures, I have gained a broader knowledge on what the principles of Biochemical Diagnosis are and how it plays a role in the diagnosis of disease.
Biochemical Diagnosis was a topic which I had found beneficial as after learning this topic I now have the capability to apply the knowledge learnt to my day to day practice but also by understanding the importance of Biochemistry Analysis I can understand what test results mean ad what the importance is in diagnosis.

Provide examples of Metabolic Disorders and briefly discuss this below.
Disease Defective Enzyme or System Symptoms Treatment

Phenylketonuria (PKU) Phenylalanine Hydroxylase severe mental retardation screening; dietary adjustment
Malignant PKU Biopterin Cofactor neurological disorder —
Type 1 tyrosinemia Fumarylacetoacetate Hydrolase nerve damage, pain, liver failure liver transplantation; preceding enzyme inhibitor plus dietary adjustment
Type 2 tyrosinemia Tyrosine Aminotransferase irritation to the corneas of the eyes diet with reduced phenylalanine and tyrosine content
Alkaptonuria Disorder of Tyrosine breakdown progressive arthritis and bone disease; dark urine —
Homocystinuria and Hyperhomocysteinemia cystathionine-?-synthase or methylenetetrahydrofolate reductase or various deficiencies in formation of the Methylcobalamin form of vitamin B12 hypercoagulability of the blood; vascular episodes; dislocation of the lens of the eye, elongation and thinning of the vitamin B12, folic acid, betaine, a diet restricted in cysteine and methionine

References
Glycogen Storage Disease Type III
Synonyms: Cori Disease, Debrancher Deficiency, Forbes Disease, GSD III
Aditi Dagli, MD, Christiaan P Sentner, MD, and David A Weinstein, MD, MMSc.
Initial Posting: March 9, 2010; Last Update: December 29, 2016. https://www.ncbi.nlm.nih.gov/books/NBK26372/
With reference to the article, it had stated how Glycogen Storage Disease type III (GSD III) is characterized by variable liver, cardiac muscle and skeletal muscle involvement.
GSD III was seen as the most common subtype which was present in approcximately 85% of the affected individuals; it was told that it manifests with liver and muscle involvement, GSD IIIb with liver involvement only comprised about 15% of all GSD III.
The article further explained that in infancy and early childhood, the liver involvement presents as ketotic hypoglycaemia, hepatomegaly, hyperlipidaemia and elevated hepatic transaminases. Liver disease becomes less prominent in adolescence and adulthood. It was told that hypertrophic cardiomyopathy develops in a majority of those with GSD IIIa usually during childhood. The clinical significance however ranges from asymptomatic in a majority to severe cardiac dysfunction, congestive heart failure and (rarely) sudden death. It was told that skeletal myopathy manifesting as weakness was not usually evident in childhood but slowly it progresses which typically becomes prominent in the third to fourth decade.
In regards to diagnosis and testing, hepatomegaly, ketotic hypoglycaemia with fasting and elevated serum concentrations of transaminases and CK are hallmarks of GSD III. The serum CK however may not be elevated at the time of the diagnostic work up but the absence of lactic acidosis and markedly elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT) concentrations may give clues to the diagnosis. The measurement of fasting serum concentration of the glucose after glucagon administration can be used to help the diagnosis; however the glucagon administration should not cause the glucose concentration to rise following the prolonged fast but it should be done so after a fast of two hours or less. The article stated that the diagnosis is established by the identification of Biallelic pathogenic variants in AGL.
In reference to this article, it was told that a high-protein diet and frequent feeds (every 3-4 hours) to maintain euglycemia which is the mainstay of the management in infancy. The article further explains how fructose and galactose can be used but however special formulas are not required, it is told that towards the end of the first year of life, one to three daily doses of 1g/kg of corn-starch can be used to avoid hypoglycaemia the protein intake of 3g/kg is recommended. Glycosade extended-release corn-starch can be used however for those who cannot make it through the night on protein and corn-starch. The article further explained how individuals who have severe hepatic cirrhosis, liver dysfunction and/or hepatocellular carcinoma have liver transplantation reserved. Liver transplantation was described to exacerbate myopathy and cardiomyopathy.

Curr Mol Med. 2002 Mar;2(2):167-75.
Molecular characterization of glycogen storage disease type III.
Shen JJ1, Chen YT. nlm.nih.gov/pubmed/11949933
In reference to the article, it has been told that the deficiency of the glycogen debranching senzyme (gene, AGL) is the causation of glycogen storage disease type III (GSD- III) which is an automosal recessive disease affecting glycogen metabolism. It shown that most GSD- III patients have AGL defiency within the liver and muscle (type llla), however some have this within their liver and not muscle (type lllb). The cloning of human AGL cDNAs and determination of the genomic structure and mRNA isoforms of AGL have allowed studies of GSD-lll at the molecular level. However the resulting information had greatly facilitated the understanding of the storage disease with remarkable clinical and enzymatic variability. With this review it was summarized by researchers that all 31 GSD-lll mutations in the literature and discuss the clinical and laboratory implications. The article described how most of the mutations were nonsense mutations which were caused by a nucleotide substitution or small insertion or deletion; it was written in the article that only one is caused by missense amino acid change, as I read further it was told that some vital genotype-phenotype correlation have emerged in particulate that exon 3 mutations (17delAG and Q6X) which were specifically associated with GSD-lllb. The test had shown that three other mutations appeared to have had some phenotype correlation, the spilice mutation IVS32-12A;G was specifically founded in GSD-lll patients who had mild clinical symptoms whilst mutations 3965delIT and 4529insA were connected with severe phenotype and early onset of clinical manifestations. It was shown that a molecular diagnostic scheme has been proposed to diagnose GSD-lll noninvasively, the characterisation of AGL mutations in GSD-lll patients had helped the structure function analysis of the bifunctional enzyme for glycogen metabolism.

Curr Mol Med. 2002 Mar;2(2):121-43.
Type I glycogen storage diseases: disorders of the glucose-6-phosphatase complex.
Chou JY1, Matern D, Mansfield BC, Chen YT https://www.ncbi.nlm.nih.gov/pubmed/11949931

With reference to this article it showed that Glycogen storage disease type I (GSD-I) is a group of autosomal recessive disorders with an incidence of 1 in 100,000. I had found that there were two major subtypes are GSD-Ia (MIM232200), caused by a deficiency of glucose-6-phosphatase (G6Pase), and GSD-Ib (MIM232220), which were caused by a deficiency in the glucose-6-phosphate transporter (G6PT). However both G6Pase and G6PT are linked with the endoplasmic reticulum (ER) membrane. G6PT translocates glucose-6-phosphate (G6P) from the cytoplasm into the lumen of the ER, where G6Pase hydrolyses the G6P into glucose and phosphate. Further on the article read developed on how together G6Pase and G6PT maintain glucose homeostasis. G6Pase is expressed in gluconeogenic tissues, the liver, kidney and intestine. However G6PT, which transports G6P efficiently only in the presence of G6Pase, which is expressed ubiquitously. I had found that this suggested that G6PT could play other roles in tissues lacking G6Pas, both GSD-Ia and GSD-Ib patients manifest phenotypic G6Pase deficiency, characterized by growth retardation, hypoglycemia, hepatomegaly, nephromegaly, hyperlipidemia, hyperuricemia, and lactic academia and the current treatment is a dietary therapy. GSD-Ib patients who also suffer from chronic neutropenia and functional deficiencies of neutrophils and monocytes, which is treated with granulocyte colony stimulating factor to restore myeloid function. The GSD-Ia and GSD-Ib genes are then cloned. It has been written in the article to date that 76 G6Pase and 69 G6PT mutations have been identified in GSD-I patients. A database of the residual enzymatic activity retained by the G6Pase missense mutants is facilitating the correlation of the disease phenotype with the patients’ genotype whilst the molecular basis for the GSD-I disorders are known and symptomatic therapies which are available in various aspects of the diseases which are poorly understood, and have no cures. Recently developed animal models of the disorders are now thought to be exploited to delineate the disease more precisely and develop new, more causative therapies.

Lucchiari S, Santoro D, Pagliarani S, Comi GP. Clinical, biochemical and genetic features of glycogen debranching enzyme deficiency. Acta Myol. 2007;26:72–4. https://www.ncbi.nlm.nih.gov/pubmed/17915576

J Inherit Metab Dis. 2015 May;38(3):511-9. doi: 10.1007/s10545-014-9772-x. Epub 2014 Oct 7.
Type I glycogen storage diseases: disorders of the glucose-6-phosphatase/glucose-6-phosphate transporter complexes.
Chou JY1, Jun HS, Mansfield BC. https://www.ncbi.nlm.nih.gov/pubmed/25288127

1st November 2017 – Learning Topic 7: Reproductive Genetic Counselling
I had found that revising this topic on Reproductive Genetic Counselling was useful as although I have knowledge on this topic already due to previous studying, a refresher was needed.
I had found that this topic (Genetic Testing, what is your view?) was one of many which was interesting due to the discussions which it had led to which made it more interesting to learn as various viewpoints were put forward.
As having the role of a Biomedical Scientist, it is important to understand the new techniques put forward as this would help me tackle everyday situations in a new way but also it is important for me to ensure that I have new knowledge which can then be brought forward into my work which would help me develop accurate and better results leading to better diagnosis and prognosis.
As a biomedical scientist it is important to keep update with new techniques and knowledge because as a biomedical scientist you are continuously developing knowledge and new skills throughout your career.
What are the different types of Genetic Tests?
? Newborn screening- This is one example of genetic testing which is used
just after birth to identify genetic disorders which can be treated early. Examples of diseases that are tested in newborn screening include: Phenylketonuria which is a genetic disorder which causes intellectual disability if left untreated. Congenital Hypothyroidism is another example of a disease which is tested in new born screening which looks at the disorder of the thyroid gland.
? Diagnostic Testing- This is used for identifying and ruling out a specific genetic or chromosomal condition.
? Carrier Testing- This is used for identifying individuals who carry one copy of a gene mutation, when the gene is present in two copies; it can cause a genetic disorder. Carrier testing is offered to individuals who have a family history of genetic disorders and in certain ethnic groups who have an increased risk of specific genetic conditions. If both parents are tested, the test can provide information about a couple’s risk of having a child with a genetic condition, such as Thalassemia.
? Prenatal Testing – This is used for the detection of changes in a fetus’s genes or chromosomes before birth. This type of genetic testing is offered during pregnancy and helps in identifying if there is an increased risk that the baby will have a genetic or chromosomal disorder.

References
Available at http://onlinelibrary.wiley.com/doi/10.1111/j.1399-0004.1988.tb02893.x/full Accessed on 1st November 2017
Evaluation of genetic counselling: recall of information, post-counselling reproduction, and attitude of the counselees Authors M. Somer, H. Mustonen, R. Norio

In reference to the article above, it had shown that the families who had recieved genetic counselling between 1972 and 1981, 791 had answered to a questionnaire which had covered recall information, post-counselling reproduction and attitudes towards counselling and prenatal diagnosis. The article included further data on the 80% who had adequate knowledge of mode of mode of inheritance along with 74% of recurrence risk. It was shown that the knowledge of mode of inheritance was poorest in multifactorial transmission (63%) and knowledge of recurrence risk in X?chromosomal disorders (61%). Forty?five per cent of the families had started a pregnancy after the counselling, but however thhe variation was between 57% (risk –25%). Early lethality of the disorder and feasibility of a prenatal study contributed to positive reproductive decisions. It was shown that 9% of chikdren who were bron after counselling were affected by the disorder in question, the observed risks had matched well with the expected one. The further 62% of respondents had felt that the counselling had a either a great or moderate impact on their reproductive plans whereas 40% expressed a wish to hear the counsellor’s opinions in addition to the facts provided. This was seen to be more common when the disorder was severe as although mpst couples (52%) wished to have a prenatal study if feasible and abort an affected foetus the 16% of ones asked were against abortion in such a case whereas the remaining 31% wished to have the study but were ambiguous about an abortion.

– Available at https://www.nature.com/articles/nrg754, Accessed on 1st November 2017. Genetic counselling and customary consanguineous marriage Bernadette Modell ; Aamra Darr
–
With reference to the article above it states Consanguineous marriage is customary in many societies but however it leads to increased prevalence of infants with severe recessive disorders. It has often been proposed that consanguineous marriage should be discouraged on medical grounds but however several expert groups have pointed out that this proposal is inconsistent with ethical principles of genetic counselling which overlooks the social importance of consanguineous marriage and has been ineffective. However instead it is suggested that custom increases the possibilities for effective genetic counselling and recommend a concerted effort to identify families at increased risk and to then provide them with risk information and carrier testing when feasible.

Reproductive genetic counselling in non?mosaic 47,XXY patients: implications for preimplantation or prenatal diagnosis: Case report and review. Gérard Tachdjian?,
Nelly Frydman, Nicole Morichon?Delvallez, Anne Le Dû, Renato Fanchin, Michel Vekemans,
René Frydman. Human Reproduction, Volume 18, Issue 2, 1 February 2003, Pages 271–275. Avaiable at https://academic.oup.com/humrep/article/18/2/271/639206. Accessed on 1st November 2017
With reference to the article, it had described with incidence of ~1 in 500 new-born males, the 47 XXY genotype was one of the most common sex chromosome abnomalies which was also most frequent in the genetic cause of human infertility. The article developed how some non-mosaic 47 XXY patients have sperm production which allows infertility treatment offered by ICSI which therefore the risk of transmitting a chromosome anomaly to the next upcoming generation was an important problem in reproductive genetic counselling of these patients. The article included a report on a twin pregnancy where there were two karyotypically normal neonates 46 XX and 46 XY were born after using ICSI in assisted reproduction of a patient with a non-mosaic 47 XXY syndrome. The article specified how to date only 38 evolving pregnancies including present cases had been reported after ICSI using sperm from non-mosaic 47 XXY patients but the article has stated that although this data was scarce, they had suggested that the risk of chromosome anomaly in the offspring of these patients was low hence their reproductive genetic counselling can be reassuring and management of the pregnancy can proceed with caution.

Aran, B., Blanco, J., Vidal, F., Vendrell, J., Egozcue, S., Barri, P.N., Egozcue, J. and Veiga, A. (1999) Screening for abnormalities of chromosomes X, Y and 18 and for diploidy in spermatozoa from infertile men participating in an in vitro fertilisation ICSI program. Fertil. Steril. , 72, 696–701. Available at http://www.fertstert.org/article/S0015-0282(99)00307-6/abstract Accessed on 1st November 2017

Aboulghar, H., Aboulghar, M., Mansour, R., Serour, G., Amin, Y. and Al?Inany, H. (2001) A prospective controlled study of karyotyping for 430 consecutive babies conceived through intracytoplasmic sperm injection. Fertil. Steril. , 76, 249–253. Available at http://www.fertstert.org/article/S0015-0282(01)01927-6/abstract Accessed on 1st November 2017

2nd November 2017 -Learning Topic 8: Prenatal Sampling
The topic on Prenatal Sampling was a topic amongst many which I had found interesting and enjoyable to learn. I believe this is a topic which was important to understand as by understanding the basic terms associated with Prenatal Sampling and the several types of prenatal sampling I would be able to apply this to my everyday work as I would understand why prenatal sampling would be requested and how this would help with the diagnosis.
It is amongst one of the important roles of a Biomedical Scientist to understand how disease is caused.
Discuss the process of Amniocentesis
Amniocentesis which is also referred as an amniotic fluid test or AFT is one of the processes used in prenatal diagnosis of chromosomal abnormalities such as neural tube defects like for instance spina bifida and anencephaly; this is a process which involves a small amount of amniotic fluid which contains fetal tissues which is then sampled from amniotic fluid which contains fetal, this is then sampled from the amniotic sac which surrounds the developing fetus. This involves a needle being passed into amniotic cavity at 14 weeks of gestation, the amniotic fluid which contains the fetal cells is cultured for chromosome analysis, biochemical analysis and molecular biological analysis.

References

– http://www.nejm.org/doi/full/10.1056/NEJM197901253000402
Prenatal Genetic Diagnosis in 3000 Amniocenteses
Mitchell S. Golbus, M.D., William D. Loughman, Ph.D., Charles J. Epstein, M.D., Giesela Halbasch, John D. Stephens, M.D., and Bryan D. Hall, M.D.
Regarding the article above it had stated that 3000 consecutive amniocenteses for prenatal diagnosis were assessed for a variety of elements such as the frequency of abnormalities, safety of the procedure, technical and interpretive difficulties and the overall accuracy of diagnosis. The article further elaborated on how chromosomal abnormalities were detected in 2.4% of 2404 pregnancies tested due to the advanced maternal age (35 years), in 1.2% of 240 monitored because of prior trisomy 21 and 9.1% of the 55 examines for other cytogenetic indications. When reading further I had found out that Mosaicism was founded in 0.4% and unexpected translocations in 0.4% but also amniotic fluid was obtained in the first attempt in 99.3% of the last 1000 cases and cultures established from 99.7% of patients attending to the clinic. Further on in the article it has stated how the fluid discolored in 1.2% of patients a quarter who had abortions however the rate of spontaneous abortion after amniocentesis was 1.5%.
Also, in the article it went on further developing the test taken showing how there were 14 diagnostic errors six of which were serious enough to affect the outcome of the pregnancy. The karyotype error rate was shown as 0.07% but the article had concluded that prenatal diagnosis was safe and highly reliable and accurate.

http://onlinelibrary.wiley.com/doi/10.1002/ajmg.1380/full
Mitochondrial disorders: genetics, counselling, prenatal diagnosis and reproductive options Authors David R. Thorburn, Hans-Henrik M. Dahl
In this article it stated that many patients with mitochondrial disorders were diagnosed by finding respiratory chain enzyme defect or a mutation in the mitochondrial DNA (mtDNA). Further on the article looked at the provision of accurate counselling and reproductive options for those families but however it was complicated by the unique genetic features of mtDNA which differentiate it from Mendelian genetics. The article had used maternal inheritance, heteroplasmy, the threshold effect, the mitochondrial bottleneck, tissue variation and selection were examples provided. After reading the article fully, although there is still much to learn about mtDNA genetics, it is still possible to provide useful guidance to families with a mtDNA mutation or a respiratory chain enzyme defect. The article described a range of current reproductive options which could be considered for the prevention of transmission of mtDNA mutations including the use of donor oocytes, prenatal diagnosis (chorionic villus sampling or amniocentesis) and preimplantation genetic diagnosis as well as future options such as nuclear transfer and cytoplasmic transfer. The article elaborated that for common mtDNA mutations associated with mitochondrial cytopathies (such as NARP, Leigh Disease, MELAS, MERRF, Leber’s Hereditary Optic Neuropathy, CPEO, Kearns-Sayre syndrome, and Pearson syndrome), a summarisation on available data on recurrence risk is done which leads to discussions on the advantages and disadvantages of reproductive options.

Cederholm M, Axelsson O. A prospective comparative study on transabdominal chorionic villus sampling and amniocentesis performed at 10-13 weeks’ gestation. Prenatal Diagnosis 1997;17(4):311-7. Available at https://www.ncbi.nlm.nih.gov/pubmed/9160382

With reference to this article, it has stated that those women with single and viable pregnancies at 10 + 5 to 13 + 6 weeks gestation who had requested foetal karyotyping for maternal age, parental anxiety or previous history of chromosomal aberration were offered participation in this study. The article stated that with a transabdominal ultrasound-guided technique, early amniocentesis (EA) were performed on 147 women and chorionic villus sampling (CVS) was performed on 174. It was written in the article that spontaneous foetal loss occurred in 6.8% women in the EA group whereas in the CVS group it occurred in 1.7%. It elaborated further that this difference was significant with a confidence interval (CI) of 0.6-9.6 per cent but also a significant difference in the need for repeat testing between the groups. In the EA group a repeat test was required in 19.0 per cent due to culture and sample failures, while 5.2 per cent of the women in the CVS group needed repeat testing because of ambiguous results. This prospective study comparing EA and CVS shows that the risk of foetal loss is higher and repeat testing is needed more after EA.
Maternal complications following amniocentesis and chorionic villus sampling for prenatal karyotyping. Maria Cederholm, Bengt Haglund,Ove Axelsson. Volume 110, Issue 4
April 2003 Pages 392–399 Available at http://onlinelibrary.wiley.com/doi/10.1046/j.1471-0528.2003.02091.x/full

Chorionic villus sampling and amniocentesis. Brambati, Bruno; Tului, Lucia. Current Opinion in Obstetrics and Gynecology: April 2005 – Volume 17 – Issue 2 – p 197–201. Available at https://journals.lww.com/co-obgyn/Abstract/2005/04000/Chorionic_villus_sampling_and_amniocentesis.16.aspx

3rd November 2017 -Learning Topic 9: Clinical Application of Linkage
The topic on Clinical Applications of Linkage was helpful to go over again as although I have already learnt about this aspect, learning it again helped me refresh myself on the understanding of Clinical Application of Linkage. A sound understanding on this particular topic would help me as a Biomedical Scientist develop further within my work field as I would have a better, updated understanding of this topic which would therefore allow me to present accurate and reliable results.
What are the types of mutations, briefly discuss these.
Substitution A substitution is a mutation which exchanges one base for another base, for example: a change in a single “chemical letter” such as switching an A to a G. Such a substitution could;
1. Change a codon to one that encodes a altered amino acid and cause a small change in the protein produced. For example, sickle cell anaemia is caused by a substitution in the beta-haemoglobin gene, which changes a single amino acid in the protein produced.
2. Change a codon to one that encodes the same amino acid and causes no change in the protein produced. These are known as “silent mutations”.
3. Change an amino-acid-coding codon to a single “stop” codon which would cause an incomplete protein, which would not function.

Insertion
Insertions are mutations are mutations where extra base pairs are inserted into a new place into the DNA.

Deletion
Deletions are mutations that result in section of DNA which is lost or deleted.

Frameshift
Protein-coding DNA is divided into codons which are three bases long, insertions and deletions can alter a gene which can result in the messages no longer being correctly described. These changes are known as frameshifts.

References

– http://annals.org/aim/article-abstract/694256/human-gene-mapping-genetic-linkage-clinical-applications?volume=93;issue=3;page=469
Human Gene Mapping, Genetic Linkage, and Clinical Applications ROBERT S. SPARKES, M.D.; M. ANNE SPENCE, Ph.D.; T. MOHANDAS, Ph.D.; LARRY J. SHAPIRO, M.D.; STEVEN J. FUNDERBURK, M.D.

With reference to this article it showed the concern of human gene mapping with the assignment of individual genes to specific parts of chromosomes. The article developed on the rapid progress within this field had shown the importance of genetics to human biology and clinical medicine. The article presented several approaches which are made available for expanding the human gene map, the gene dosage approach is however used in the mapping of the esterase D and retinoblastoma locus on the long arm of chromosome 13. The article expressed how principles behind kindred linkage analysis and the application of somatic cell hybridization techniques are examined in relation to human gene mapping, as well as this the article referred to recent data on the steroid sulfatase gene which had suggested that not all X-linked genes are susceptible to inactivation, various clinical applications of human gene mapping and linkage information were presented. The article also stated that with the application of current molecular techniques, the human gene map may be substantially completed by the end of the century.
– http://jmg.bmj.com/content/38/3/193

In regards to the article I had found that familial hypertrophic cardiomyopathy (FHC) is a prevalent inherited disease which is characterised by unexplained hypertrophy of the heart muscle. The article referred to how clinical manifestations were heterogeneous and how the disease was a leading cause of sudden cardiac death amongst the young as well as those who are healthy. It was shown that more than 120 different mutations had been reported to be the following genes encoding sarcomeric polypeptides given in parentheses: TNNT (troponin T), MYL3(essential myosin light chain), MYH6 (? myosin heavy chain), MYBPC3 (myosin binding protein), MYL2 (regulatory myosin light chain) TPM1) TPM1 (? tropomyosin),ACTC (? cardiac actin), andTNNI3 (troponin I). As reading further on, the article elaborated on a disease locus on chromosome 7 which had been linked to FHC but however the gene was not yet identified. In addition to this the disease genes were thought to remain discovered since two recent studies found that it was only possible to genotype 50-60% of the FHC population by mutation analyses of 7 disease gene. It was thought to said that to optimise risk stratification and management of FHC patients, it is vital to identify all disease carriers but this is difficult by physical examination because of the age dependent penetrance of the disease. Although the disease carriers may be identified by the use of genetic diagnosis as although it is laborious due to the large number of disease genes and the pronounced allelic heterogeneity of the disease loci, with the majority affected families having their own “private ” missense mutation. In reference to this it was seen that genetic diagnosis was complicated due to the fact that several amino acid polymorphisms occur in most of the FHC genes8 9 (unpublished observations). In addition to this, given this complex genetic background, the use of linkage analysis could be beneficial as it could potentially identify the most likely disease gene and provide evidence for exclusion of some or all of the other candidate disease loci even in small families.
The article stated how the aim of the present study was to develop a firm basis for efficient use of linkage genetic diagnosis of FHC by a well founded selections of polymorphic markers defining 9 FHS loci including a refined genetic mapping of the troponin T gene in a 4 cM interval. The article concluded how for rapid analysis multiplex PCR panels were developed comprising all selected markers. The feasibilitiy of the method was evaluated by the identification of mutations within the 3 families of varying size.

https://www.nature.com/articles/nrg3908

Within this article it stated how for many years linkage analysis was the primary tool which was used for genetic mapping of Mendelian and complex traits with familial aggregation. The article describes how linkage analysis was largely supplanted by the wide adoption of genome-wide association studies (GWASs but however with the recent increased use of whole-genome sequencing (WGS), linkage analysis is emerging once again as an important and powerful analysis method for the identification of genes involved within disease aetiology, often in conjunction with WGS filtering approaches. The article reviewed the principles of linkage analysis which had provided practical guidelines for carrying out linkage studies using WGS data.

Bailey-Wilson, J. E. ; Wilson, A. F. Linkage analysis in the next-generation sequencing era. Hum. Hered. 72, 228–236 (2011). https://www.ncbi.nlm.nih.gov/pubmed/22189465?dopt=Abstract;holding=npg

McClellan, J. ; King, M. C. Genetic heterogeneity in human disease. Cell 141, 210–217 (2010). https://www.ncbi.nlm.nih.gov/pubmed/20403315?dopt=Abstract;holding=npg
4th November 2017 -Learning Topic 10: DNA Sequencing
I had found the topic of DNA Sequencing interesting as I had enjoyed this topic overall. I think it is important to understand the importance of the basic terms associated with DNA Sequencing as well as being able to understand the importance of DNA Sequencing.
This supports me with my daily practice as a Biomedical Scientist as it helps me to consider certain case studies where abnormal results are present which allows me to further investigate why the certain results were abnormal, but I would know what mechanisms play a part in the disease as well as this I would be able to investigate other tests.
When judging this topic overall, I believe it is one of the fascinating topics to learn as DNA Sequencing plays a vital part in the job role of a Biomedical Scientist which is to find the cause of disease and to understand which mechanisms are involved in this procedure.
What is your understanding of the term DNA Sequencing?
DNA Sequencing is the name which is given to the process which determines the exact order of nucleotides within a DNA molecule. This uses any procedure to determine the order of the four bases, the four bases include Adenine, Guanine, Cytosine and Thymine within a strand of DNA.

References
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC392330/
Maxam Gilbert Method

With regards to the referenced article above, it is told that DNA can be sequenced by a chemical procedure which breaks a terminally labelled DNA molecule partially at each repetition of a base. The article carries on explaining the lengths of the labelled fragments which identify the positions of the base, the article described reactions which cleave DNA preferentially at Guanines, at Adenines, at Cytosines and Thymine equally and at Cytosines alone. The authors of the article explained that when the products of the four reactions are resolved by size and electrophoresis on a polyacrylamide gel the DNA sequence can be read from the pattern of radioactive bands which would the permit the technique sequencing at least 100 bases from the point of labelling.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727787/
After reading the above referenced article I had found out that determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. The article included statistical data of the last fifty years where there was a large number of researchers who had applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. The time-scale had seen tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.
https://www.nature.com/articles/nbt1486
With reference to this article, I had found that DNA sequencing represents a single format onto which a wide range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms had become widely available which had reduced the cost of DNA sequencing by over two orders of magnitude and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies were rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. The article stated that the next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.
Shendure, J., Mitra, R.D., Varma, C. ; Church, G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5, 335–344 (2004). Available at https://www.ncbi.nlm.nih.gov/pubmed/15143316?dopt=Abstract;holding=npg

Adessi, C. et al. Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 28, e87 (2000). Available at https://www.ncbi.nlm.nih.gov/pubmed/11024189?dopt=Abstract;holding=npg

5th November 2017 -Learning Topic 11: Techniques – Southern Blotting, and PCR
Techniques – Southern Blotting and PCR were the other topics studied which I had found fairly interesting and enjoyable. After studying these topics thoroughly, I understood the importance of Southern Blotting and PCR.
It is important for a Biomedical Scientist to understand the different techques used to help with identifying the causation of disease as this is amongst the major roles of a Biomedical Scientist and having learnt this topic I have a clear understanding of basic tests that are used
This helps with my daily practice as a biomedical scientist by allowing me to consider certain techniques for certain tests.
Overall, I think this topic is fascinating to learn as this topic plays a part in a biomedical scientist’s job role which is to find the cause of disease.

Discuss the process of PCR
PCR is referred to a DNA polymerase reaction which as with any polymerase reaction requires a DNA template and a free 3′-OH. The template which is provided by the DNA sample which is to be amplified and the free 3′-OH are provided by site-specific oligonucleotide primers. These primers are complementary to each of the ends of the sequence which is to be amplified, there are three main steps to the reaction, these are as followed;
1. Denaturation: The DNA is now heated to usually 95oC to render it single-stranded .
2. Annealing: This is when the two primers bind the appropriate complementary strand; the temperature for this particular step varies depending on the size of the primers and homology to the target of DNA.
3. Primer Extension: DNA polymerase now extend the primer by its polymerase activity; this is done at a temperature optimal for the specific polymerase which is being used; Taq Polymerase is through to be the popular enzyme for this step, the polymerase from the thermophilic (Heat-Loving bacteria Thermus Aquaticus; the extension is performed at 72 oC

References
– http://jcm.asm.org/content/29/3/573.short

In reference to the article a methodological study had been performed to compare the polymerase chain reaction known as PCR and Southern blot hybridization, these are two commonly used testing strategies used to detect human papillomavirus infection (HPV), the article looked at how three laboratories tested masked aliquots of exfoliated cervical cell specimens gathered from 120 females through what is called a cervicovaginal lavage. The article showed the study population which involved 32 females with condylomatous atypia or cervical intraepithelial as well as 88 women with unknown history of cervical neoplasia. The article presented two labs who used PCR with various sets of consensus primers for HPV detection whereas the third lab used low-stringency Southern blot hybridization to identify all the types of HPV. It was found that one of the PCR primer sets detected HPV types with a differential efficiency which was not predicted by analysis of DNA sequences or direct testing of HPV-containing plasmids. In addition to this second PCR primer set was seen to be a much broader consensus system used to detect HPV types as Southern blotting through requiring less clinical specimen. Statistics in the article showed that 80% of females with cervical intraepithelial neoplasia or condylomatous atypia were found to be HPV infected both by southern blotting and by the second PCR primer set whereas amongst the control women, 11% were HPV positive by Southern blotting and 31% were positive with second sets of primers. The article concluded how most of the HPV infections found only by PCR were not due to HPV types 6, 11, 16, 18, 31, 33 or 45, these HPV types were known to be uncommon amongst normal women in the study population even as determined by PCR method.
Methods. 2001 Dec;25(4):419-29.
Quantitation of viral load using real-time amplification techniques.
Niesters HG1. https://www.ncbi.nlm.nih.gov/pubmed/11846611?dopt=Abstract&holding=npg
In reference to the article it had shown real-time PCR amplification techniques which are currently in use to determine the viral load in clinical samples of increasing number targets. The article looks at how real-time PCR reduces the time necessary to generate results after amplification, the article looks at in-house developed PCR and nucleic acid sequence-based amplification (NASBA)-based systems combined with numerous detection strategies which were employed in a clinical diagnostic setting. The article looked at the importance of these assays within disease management which are still in an exploration phase as although these technologies have the implicit capability of accurately measuring DNA and RNA in clinical samples, where issues related to standardisation and quality control had to be resolved to enable routine implementation of those technologies within molecular diagnostics.

Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005). https://www.ncbi.nlm.nih.gov/pubmed/16314309?dopt=Abstract&holding=npg
In regards to the referenced article I had found that a novel microRNA (miRNA) quantification method had been developed using step-loop RT followed by Taqman PCR analysis. Stem-loop RT primers were seen better than convectional ones in terms of RT efficiency and specificity. Taqman miRNA assays are certain for mature miRNAs and discrimination amongst related miRNAs which differ by as little as one nucleotide. When reading further it showed that they were not affected by genomic DNA contamination, precise quantification was achieved routinely with as small as 25 pg total RNA for most miRNAs, the high sensitivity, specificity and precision of this particular method allowed for direct analysis of a single cell without nucleic acid purification. It was shown in the article that Like standard TaqMan gene expression assays, TaqMan miRNA assays exhibit a dynamic range of seven orders of magnitude but also the quantification of five miRNAs in seven mouse tissues showed variation from less than 10 to more than 30,000 copies per cell. It was thought that this method enabled fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases. Stem-loop RT-PCR was seen to be used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs). Furthermore, the concept of stem-loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency.

Plant Biotechnol J. 2009 Sep;7(7):621-30. doi: 10.1111/j.1467-7652.2009.00429.x. Epub 2009 Jul 13.
A novel real-time polymerase chain reaction method for high throughput quantification of small regulatory RNAs.
Yang H1, Schmuke JJ, Flagg LM, Roberts JK, Allen EM, Ivashuta S, Gilbertson LA, Armstrong TA, Christian AT. https://www.ncbi.nlm.nih.gov/pubmed/19619184

RNA. 2005 Nov;11(11):1737-44.
Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.
Raymond CK1, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM. https://www.ncbi.nlm.nih.gov/pubmed/16244135

6th November 2017 -Learning Topic 12: DNA Profiling
DNA Profiling was a topic which was new to me as this topic was one which was not studied before in my previous studying.
This learning topic was a new area and I have gained knowledge on the subject area. I enjoyed going through the lectures as this was new to me so it made it interesting as I was gaining knowledge whilst studying.
This has helped me as biomedical scientist as I am gaining knowledge and developing new skills and knowledge.
Discuss the advantages and disadvantages of DNA Profiling
There are a range of advantages and disadvantages of DNA Profiling, DNA profiling lies within specificity as even relatively minute quantities of DNA at a crime scene can yield sufficient material for analysis. At least 13 markers are typically compared from the DNA in two samples by forensic scientists but however within a test with 13 markers the probability of any two individuals whom have identical profiles is estimated to be below 1 in 10 billion. In addition to this when specimens are collected in a correct manner and the procedure is performed correctly, DNA profiling is an extremely accurate method to compare a suspect’s DNA with crime scene specimens.
Although there are advantages of this method as stated above, there are drawbacks. DNA evidence is only one of various types of evidence jurors should consider when considering a case, well-known TV shows such as “CSI” may have popularized forensic science to the point where some jurors have unrealistic expectations of DNA analysis and accord it more weight than other types of evidence, this is referred to as the “CSI Effect” but however maintaining DNA databanks can help police identify criminals but it can also pose ethical quandaries when authorities keep samples from individuals who have not been accused of any crime. DNA dragnet operations is the method known to where police gather samples from a large variety of people in a geographic region to help find a culprit, this has been proven especially controversial.

References
Multiplex pyrosequencing of InDel markers for forensic DNA analysis https://onlinelibrary.wiley.com/doi/full/10.1002/elps.201600255
In reference to this article it shows how the capillary electrophoresis (CE) technology which is commonly used for fragment length separations of markers of forensic DNA analysis. The article presented a study in which pyrosequencing technology was used as an alternative and rapid tool for the analysis of biallelic Indel (insertion/deletion) markers for individual identification. It was told that the DNA typing was based on a subset of the Indel markers which are included in the investigator DIPplex kit which is sequenced in a multiplex pyrosequencing analysis. The article elaborated that to facilitate the analysis of degraded DNA, the polymerase chain reaction (PCR) fragments were kept short in the primer design. The article also included samples from individuals of a Swedish origin which were genotype using pyrosequencing strategy and analysis of the Investigator DIPplex markers with CE. The article had also presented a comparison between the pyrosequencing and CE data revealed concordant results demonstrating a robust and correct genotyping by pyrosequencing. Optimal markers combinations and a directed dispensation strategy, were used where five markers could be multiplexed and analyzed simultaneously. any crime. DNA dragnet operations is the method known to where police gather samples from a large variety of people in a geographic region to help find a culprit, this has been proven especially controversial.

Multiplex pyrosequencing of InDel markers for forensic DNA analysis https://onlinelibrary.wiley.com/doi/full/10.1002/elps.201600255
The article presented the proof-of-principle study which had demonstrated that multiplex InDel pyrosequencing analysis was possible but however further studies which were presented in the article on degraded samples, lower DNA quantities and mixtures which were required to fully optimise InDel analysis by pyrosequecing for forensic applications. Overall it was seen that although CE analysis is implemented in most forensic labs, multiplex InDel pyrosequencing offers a cost-effective alternative for some applications.
The future of forensic DNA analysis
John M. Butler
Published 22 June 2015.DOI: 10.1098/rstb.2014.0252 http://rstb.royalsocietypublishing.org/content/370/1674/20140252
The article referenced looks at the thoughts and views of the author on the basis of field forensix DNA tetsing which had been headed for the next decade providing on where the field has come to for the past 30 years. In similarity to the Olympic motto of ‘faster, higher, stronger’, according to the article forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. The new short tandem repeat (STR) loci has seen to have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is seen to be on the verge of enabling new applications whereas the next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities which will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profile.

Advances in forensic DNA quantification: A review https://onlinelibrary.wiley.com/doi/full/10.1002/elps.201400187

The article focusses on the critical step in forensic biology: detection and quantification of human DNA biological samples. It was stated in the article that determination of the quantity and quality of the human DNA taken from biological evidence is merely important for various reasons. The first reason looks at the dependency of the source and extraction method, the quality referring to the purity and length as well as the quantity of the resultant DNA extract which however can vary greatly. This can be seen as affecting the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use such as standard short?tandem repeat (STR) typing, mini?STR typing or mitochondrial DNA sequencing. The second reason which was referred to in the article was the importance of forensic analysis to preserve as much of the evidence as possible for retesting, as it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. The last method was in reference to the results from initial quantitative and qualitative evaluations which permit a more informed interpretation of downstream analytical results. The newer quantitative techniques involving real?time PCR can potentially reveal the presence of degraded DNA and PCR inhibitors, which provide potential reasons for poor genotyping results and that may indicate methods which can be used for downstream typing success. To conclude the article it was told that the more information which was available, the easier it is would be to interpret and process the sample which would then result into a higher likelihood of successful DNA typing. There are two main goals which have been involved in the history of the development of quantitative methods, these are improving precision of the analysis and increasing the informational content of the results, i had found that the article covers advances within forensic DNA quantification methods and recent development in RNA quantification.

Gill P,
1. Jeffreys AJ,
2. Werrett DJ
.1985 Forensic application of DNA ‘fingerprints’. Nature 318, 577–579. www.ncbi.nlm.nih.gov/pubmed/3840867?access_num=3840867;link_type=MED;dopt=Abstract

Forensic DNA typing strategy of degraded DNA on discarded cigarette ends using the AmpF?STR® Identifiler®, Identifiler® Plus and MiniFiler™ PCR Amplification Kits http://www.scienceandjusticejournal.com/article/S1355-0306(14)00054-9/abstract

7th November 2017 -Learning Topic 13: Management of Genetic Disease
Management of Genetic Disease was amongst other learning topics which I had found fairly easy as this topic was easy to grasp as information provided was in depth and had helped me gain an idea of this topic quickly.
After studying the lectures carefully, I was able to gain knowledge on key areas such as what the principles of management genetic disease are and how they play a role in the diagnosis of disease.
Briefly discuss the Pathologines of Beta Thalassemia
Beta Thalassemia area is referred to the group of inherited blood disorders, these are forms of Thalassemia which are caused by reduced or absent synthesis of the beta chains of haemoglobin which result to variable outcomes varying from severe anaemia to clinically asymptomatic individuals. It is thought that Global Annual Incidence is estimated at one in 100,000, Beta Thalassemia however is caused by mutations in the HBB gene on chromosome 11 which is inherited in an autosomal recessive fashion but also the severity of the disease depends on the nature of the mutation.
Overtime HBB blockage leads to decrease beta-chains synthesis. The inability of the body to construct new beta-chains leads to underproduction of HbA, the reduction in HbA fills the red blood cells in turn leading to microcytic anaemia, the microcytic anaemia develops to inadequate HBB protein for sufficient red blood cell functioning and due to this the patient may require a blood transfusion to makeup for the blockages in the beta-chains. However repeated blood transfusions can lead to a build-up of iron overload which can then result into iron toxicity, the iron toxicity can cause numerous problems such as myocardial siderosis and heart failure gradually leading to the death of the patient.

References
Cavazzana-Calvo, M. et al. Transfusion independence and HMGA2 activation after gene therapy of human ?-thalassaemia. Nature 467, 318–322 (2010).avaiable at https://www.ncbi.nlm.nih.gov/pubmed/20844535?dopt=Abstract;holding=npg
In reference to this article it has specified that ?-haemoglobinopathies the most prevalent inherited disorders worldwide, gene therapy of ?-thalassaemia is seen particularly challenging given the requirement for massive haemoglobin production in the lineage-specific manner as well as the lack of selective advantage for corrected haematopoietic stem cells. After reading this article i had found that the compound ?(E)/?(0)-thalassaemia is the most common form of severe thalassaemia in southeast Asian countries and their diasporas. Due to the ?(E)-globin allele bearing a point mutation it causes alternative splicing. It was found that the abnormally spliced form is non-coding, whereas the correctly spliced messenger RNA expresses a mutated ?(E)-globin with partial instability but when this is compounded with a non-functional ?(0) allele, a profound decrease in ?-globin synthesis results, and approximately half of ?(E)/?(0)-thalassaemia patients are transfusion-dependent. I had found that the only available curative therapy is allogeneic haematopoietic stem cell transplantation, although most patients do not have a human-leukocyte-antigen-matched, geno-identical donor, and those who do still risk rejection or graft-versus-host disease. It was presented in the article that after 33 months the lentiviral ?-globin gene transfer, an adult patient with severe ?(E)/?(0)-thalassaemiawas dependent on monthly transfusions from a young age but now had cbecame transfusion independent for the past 21 months. It is said that bood haemoglobin is maintained between 9 and 10?g?dl(-1), of which one-third contains vector-encoded ?-globin. The article explained that most of the therapeutic benefit resulted from a dominant, myeloid-biased cell clone, in which the integrated vector caused transcriptional activation of HMGA2 in erythroid cells with further increased expression of a truncated HMGA2 mRNA insensitive to degradation by let-7 microRNAs. The clonal dominance which accompanies therapeutic efficacy may be coincidental and stochastic or result from a hitherto benign cell expansion caused by dysregulation of the HMGA2 gene in stem/progenitor cells.

Hoban, M. D. et al. Correction of the sickle cell disease mutation in human hematopoietic stem/progenitor cells. Blood 125, 2597–2604 (2015). Available at https://www.ncbi.nlm.nih.gov/pubmed/25733580?dopt=Abstract;holding=npg
With reference to the article, sickle cell disease also referred to as (SCD) is characterised by the single point of mutation in the seventh codon of the ?-globin gene. The site-specific correction of sickle mutation in the hematopoietic stem cells would allow for permanent production of the normal red blood cells. The use of zinc-finger nucleases (ZFNS) is designed to flank the sickle mutation which is demonstrated within the article showing that efficient targeted cleavage at the ?-globin locus with minimal off-target modification. Further on within the article it was shown that in the experiment co-delivering a homologous donor template (either an integrase-defective lentiviral vector or a DNA oligonucleotide), high levels of gene modification were achieved in CD34(+) hematopoietic stem and progenitor cells. Modified cells maintained their ability to engraft NOD/SCID/IL2r?(null) mice and to create cells from multiple lineages, although with a reduction in the modification levels relative to the in vitro samples. The article placed emphasis on the ZFN-driven gene correction in CD34(+) cells from the bone marrow of patients with SCD resulted in the production of wild-type haemoglobin tetramers.

Romero Z, Urbinati F, Geiger S, Cooper AR, Wherley J, Kaufman ML, Hollis RP, de Assin RR, Senadheera S, Sahagian A, Jin X, Gellis A, Wang X, Gjertson D, Deoliveira S, Kempert P, Shupien S, Abdel-Azim H, Walters MC, Meiselman HJ, Wenby RB, Gruber T, Marder V, Coates TD, Kohn DB.
J Clin Invest. 2013 Jul 1. pii: 67930. doi: 10.1172/JCI67930. Available at https://www.ncbi.nlm.nih.gov/pubmed/23863630

In reference to the article I had found out that autologous hematopoietic stem cell gene therapy was an approach used in treating sickle cells disease also referred to as SCD, however patients may result into lower morbidity than allogeneic transplantation. The article had described an experiment which had examined the potential of lentiviral vector (LV) (CCL- ?AS3-FB) encoding a human haemoglobin gene which was engineered to impede sickle haemoglobin polymerization (HBBAS3) in order to transduce human BM CD34+ cells from SCD donors which then prevents the sickling of red blood cells produced by in vitro differentiation. Further on it was told that the CCL-?AS3-FB LV transduced BM CD34+ cells from either healthy or SCD donors at similar levels, based on quantitative PCR and colony-forming unit progenitor analysis, consistent expression of HBBAS3 mRNA and HbAS3 protein compromised a fourth of the total ?-globin-like transcripts and haemoglobin (Hb) tetramers. However due to deoxygenation, a lower percentage of HBBAS3-transduced red blood cells exhibited sickling when compared with mock-transduced cells from sickle donors. The article had presented information on the transduced BM CD34+ cells which were transplanted into immunodeficient mice, which had then led to the human cells recovering after 2-3 months which were then cultured for erythroid differentiation, this showed levels of HBBAS3 mRNA similar to those seen in the CD34+ cells that were directly differentiated in vitro. After analysing the results provided in the article it was found that these results showed that the CCL-?AS3-FB LV is capable of efficient transfer and consistent expression of an effective anti-sickling ?-globin gene in human SCD BM CD34+ progenitor cells, improving physiologic parameters of the resulting red blood cells.

Gene therapy for adenosine deaminase-deficient severe combined immune deficiency: clinical comparison of retroviral vectors and treatment plans.
Candotti F, Shaw KL, Muul L, Carbonaro D, Sokolic R, Choi C, Schurman SH, Garabedian E, Kesserwan C, Jagadeesh GJ, Fu PY, Gschweng E, Cooper A, Tisdale JF, Weinberg KI, Crooks GM, Kapoor N, Shah A, Abdel-Azim H, Yu XJ, Smogorzewska M, Wayne AS, Rosenblatt HM, Davis CM, Hanson C, Rishi RG, Wang X, Gjertson D, Yang OO, Balamurugan A, Bauer G, Ireland JA, Engel BC, Podsakoff GM, Hershfield MS, Blaese RM, Parkman R, Kohn DB.
Blood. 2012 Nov 1;120(18):3635-46. doi: 10.1182/blood-2012-02-400937. Epub 2012 Sep 11. Available at https://www.ncbi.nlm.nih.gov/pubmed/22968453

Cavazzana-Calvo, M. et al. Transfusion independence and HMGA2 activation after gene therapy of human ?-thalassaemia. Nature 467, 318–322 (2010). Available at https://www.ncbi.nlm.nih.gov/pubmed/20844535?dopt=Abstract;holding=npg

8th November 2017 -Learning Topic 14: Avoidance and Prevention of Disease
The topic Avoidance and Prevention of Disease for me was quite interesting, I enjoyed the topic overall. I think it was vital to understand the importance of understanding the basics of communicable diseases and diagnostic and containment techniques.
It is vital as a biomedical scientist to understand what techquies are best to use, as this is a major role in a biomedical scientist job.
This helps with my daily practice as a biomedical scientist by allowing me to consider what techquies are appropriate to use for what test .
Overall, I think this topic is fascinating to learn as this topic plays a major role in a biomedical scientist’s job role which is to find the cause of disease by using appropriate techquies.
Describe the method of ELISA
The basic enzyme-linked immunosorbent assay (ELISA), or enzyme immunoassay is distinguished from other antibody-based assays because separation of specific and non-specific interactions occurs via serial binding to a solid surface, usually a polystyrene multiwell plate, because quantitative results can be achieved.
The ELISA procedure results in a colored end product which correlates to the amount of analyte present in the original sample. ELISAs are quick and simple to carry out, and since they are designed to rapidly handle a large number of samples in parallel, they are a very popular choice for the evaluation of various research and diagnostic targets.
ELISAs begin with a coating step, where the first layer, either an antigen or an antibody, is adsorbed to a well in an ELISA plate. Coating is followed by blocking and detection. Since the assay uses surface binding for separation, several washes are repeated between each ELISA step to remove unbound materials. During this process it is essential that excess liquid is removed in order to prevent the dilution of the solutions added in the next stage. For greatest consistency specialized plate washers are used. ELISAs can be quite complex, including various intervening steps and the ability to measure protein concentrations in heterogeneous samples such as blood. The most complex and varying step in the overall process is detection, where multiple layers of antibodies can be used to amplify signal.

Reference
http://rstb.royalsocietypublishing.org/content/319/1194/361.long
With reference to the article it had showed that the preceding papers had been dealt with major advances in the understanding and detecting of mutational basis of human disease. The article looked at how if these advances were to be of a practical benefit, systems of effective, efficient and acceptable delivery of the technology to the relevant population groups would need to be planned. It was developed further that within these delivery systems, the key figure is likely to be the clinical geneticist which is somewhat a shadowy figure referred to either a doctor amongst scientists or a scientists amongst doctors. A clinical geneticist acts as a user-friendly interface between the public and the conceptually quite difficult fields of modern genetics. when reading on the article referred to how just a Few people in this age of transition of computer literacy will underestimate the importance of a user-friendly interface, without which even the most powerful analytical machines are underused, error prone, or even incomprehensible.

https://www.jstor.org/stable/2396674?seq=1#page_scan_tab_contents
In reference to the article above it had showed recent studies of the effects of disease which can only b reduced by prevention and treatment. After reading the article I had found out that it is now possible for interrupt development after foetal diagnosis, this then prevents births but however this is not the causation of disease, but it is usefully termed as “avoidance.” There consequences to genetic disorder of mutational events in the past including remote and the immediate past and prevention but in true sense it can only be applied to preventing further mutations. Knowledge is a requirement for both of the mechanism of mutation and of the mutagens which populations and individuals are exposed to as well as the maintenance of public health requiring the gathering of relevant data ti mutational disease.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449675/
With reference to the above article it was found that preimplantation genetic diagnosis was developed nearly a quarter-century ago, preimplantation genetic diagnosis was introduced as an alternative form of prenatal diagnosis which is carried out on embryos. Preimplantation genetic diagnosis was offered for diagnosis in couples who were at risk of single gene genetic disorders such as Spinal Muscular Atrophy, Cystic Fibrosis and Huntington Disease, PGD was seen as the most frequently employed in assisting reproduction of the detection of chromosome aneuploidy from advancing maternal age or even structural chromosome rearrangements. Further on the article looks at the major improvements which had been seen in PGD analysis with movement away from older, less effective technologies like fluorescence in situ hybridisation (FISH) to newer molecular tools like DNA microarrays and next generation sequencing. After further reading the article, the article mentioned how improved results showed as with the decreasing use of Day 3 blastomere biopsy in favour of polar body or Day 5 trophectoderm biopsy. The article raised discussions regarding scientific, ethical, legal and social issues surrounding the use of sequence data from embryo biopsy which had started and must continue to avoid concern regarding eugenic or inappropriate use of this particular technology.
The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria
XZ Li, P Plésiat, H Nikaido – Clinical microbiology reviews, 2015 – Am Soc Microbiol http://cmr.asm.org/content/28/2/337.short

Gram-Negative Bacteria
K Tuwairqi – Encyclopedia of Ophthalmology, 2018 – Springer https://link.springer.com/content/pdf/10.1007/978-3-540-69000-9_796.pdf

9th November 2017 -Learning Topic 15: Ethical and Social Issues in Clinical Genetics
This topic was a good refresher, as I had an understanding on Ethical and Social Issues in Clinical Genetics already from previous studying. I found it useful to revise the topic Bioethics of stem cell research.
As a biomedical scientist it’s vital to understand the importance consent and confidentiality as this plays a major role in a biomedical scientist’s job role. This topic was useful as I can apply this knowledge to my daily practice as well as being able to develop as a biomedical scientist.
Discuss below the advantages and disadvantages of Genetic Testing.
Disadvantages of Genetic Screening
There are a range of drawbacks of genetic screening, many people feel that genetic screening leads to discrimination of those who have “inferior” genes, this is one of the disadvantages. As well as this genetic screening is thought to lead to reproductive decisions being based on the genetics of their child. As well as this many individuals, feel that the use of genetic screening will alter the ways humans reproduce as instead of allowing reproduction to take place naturally, people could use Foetal Embryonic Genetic Screening to select for a better child. This has caused arguments between society as they believe this is playing with God as they are choosing what is best for their child, many religious people have disagreed to this and believed that it was a blasphemy. Abortion is another factor which has been considered as parents may consider an abortion if they find out their child has defects, this is seen as a major drawback of genetic screening.
Advantages of Genetic Screening
Screening for genetic abnormalities allows doctors to prescribe initial treatment to a patient as they will already have a clear understanding of what the disease is therefore leading to the patient living a longer productive life. For instance, if a patient was found positive for a cancer-causing gene the patient could modify their behaviour to prevent the expression of the gene. However, it has been argued that a person may not want to know if they were predisposed for a condition which was untreatable, although this argument is true it can be argued that if one was to know about their illness then they would make alterations in their life to deal with this condition giving them more time.

References
Addressing the Ethical Challenges in Genetic Testing and Sequencing of Children
Ellen Wright Clayton , Laurence B. McCullough , Leslie G. Biesecker , Steven Joffe , Lainie Friedman Ross , Susan M. Wolf & For the Clinical Sequencing Exploratory Research (CSER) Consortium Pediatrics Working Group show all
Pages 3-9 | Published online: 04 Mar 2014 https://www.ncbi.nlm.nih.gov/pubmed/23428972?dopt=Abstract

With reference to the above article, I had found that the genetic testing and genetic screening of children are common. The article looks at decisions on whether to offer genetic testing and screening should be driven by the interest of the child, the article looks at the growing literature on psychosocial and clinical effects of such testing and screening which can help inform the best practices. Further on the article includes reference to the policy statement recommendations which were developed collaboratively by American Academy of Pediatrics and the American College of Medical Genetics and Genomics in respect to various scenarios in which genetic screening and testing can take place.

2011 May;18(3):148-62. doi: 10.1080/08989621.2011.575033.
A clinical perspective on ethical issues in genetic testing.
Sijmons RH1, Van Langen IM, Sijmons JG. https://www.ncbi.nlm.nih.gov/pubmed/21574071

In regards to the article reference, I had found that genetic testing was traditionally preceded by counselling to discuss the main advantages and disadvantages with people to help them make informed decisions. This new technique was explained in the article as the whole genome and exome sequencing which was currently only being used in research settings which can identify many gene mutations including substantial numbers of mutations with unknown pathological effect; which may threaten the balance approach if it was used in clinical setting. The article discussed the ethical challenges of several approaches to pre and posts natal DNA testing, individual privacy versus the interests of families and of scientists as well as the clinician’s duty to re-contact if new information or options become available.
A statement of reaffirmation for this policy was published at
• 123(5):1421
• 115(5):1438
Pediatrics
June 2001, VOLUME 107 / ISSUE 6
From the American Academy of Pediatrics
AMERICAN ACADEMY OF PEDIATRICS
Ethical Issues With Genetic Testing in Pediatrics
Committee on Bioethics http://pediatrics.aappublications.org/content/107/6/1451?utm_source=TrendMD;utm_medium=TrendMD;utm_campaign=Pediatrics_TrendMD_0

In reference to the article it shows the advances in genetic research which promises great developments in the diagnosis and treatment of many childhood diseases. In the article it says that emerging genetic technology often enables testing and screening post the development of definitive treatment or preventive measures, in such circumstances careful consideration is needed to give testing and screening of children to ensure that the usage of this technology promotes the best interest of the child. The article refers to the statement reviewing the considerations for the use of genetic technology for newborn screening, carrier testing and testing for susceptible to late-onset conditions. The article refers to the recommendations which are made to promoting informed participations by parents for newborn screening and limited use of carrier testing and testing for late-onset conditions within the paediatric population. The article develops on how this particular area of medicine is encouraged through additional research and education.
AAP Grand Rounds
September 2013, VOLUME 30 / ISSUE 3
New Guidelines on Genetic Testing and Screening in Children
Rizwan Hamid http://aapgrandrounds.aappublications.org/content/30/3/36?utm_source=TrendMD;utm_medium=TrendMD;utm_campaign=AAPGrandRounds_TrendMD_0

Technical report: ethical and policy issues in genetic testing and screening of children
• Laine Friedman Ross MD, PhD1, 2, 3
• , Howard M. Saal MD3
• , Karen L. David MD, MS4, 6
• ; Rebecca R. Anderson JD, MS5
• …
• and the American Academy of Pediatrics; American College of Medical Genetics and Genomics
• – Show fewer authors
• Genetics in Medicine volume 15, pages 234–245 (2013)
• doi:10.1038/gim.2012.176 https://www.nature.c