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Lab 1 Assessment

Your Lab assessment now requires you to find a 2 recent research references on fertilisation or in vitro fertilisation.

Paste each reference on your page, as shown in the class.

Write below each reference a brief summary of the research article methods and findings.

The summary for each need not be more than 3-4 paragraphs in length.

This will need to be completed before next weeks laboratory.

The use of r-hFSH in treatment of idiopathic male factor infertility before ICSI.

look at this

PMID 26166637

The objective of this investigations was to evaluate whether or not the pre-treatment use of Recombinant Human Follicle Stimulating Hormone (r-hFSH), could be used to treat common male infertility issues as Idiopathic Oligozoospermia, to improve their clinical results of Intracytoplasmic Sperm Injection (ICSI).

They selected a sample of 82 couples that were infertile due to the Idiopathic male factor, from the Biofertility Center in Rome, Italy between May 2013- April 2014 and randomly selected a treatment group of 36 males, Group A, and control group of 46 men, Group. The men in treatment Group A were subcutaneously injected with 150 IU of R-hFSH; Gonad F© (recombinant Human FSH) 3 times per week, for a 3 month period. The subjects in the control Group B were injected with a placebo and therefore received no treatment. After the three month period all 82 couples underwent a cycle of ICSI. In each group fertilisation, rate of implantation, rate of clinical pregnancy and the rate of miscarriage were assessed.

They found that the rate fertilisation was comparable in both treatment groups, although treatment group A had a significantly higher implantation rate and clinical pregnancy rate as well as a statistically significant lower rate of miscarriage (P<0.05). The conclusion that they drew was that the treatment use of r-hFSH to treat Idiopathic males infertility prior to ICSI can improve the clinical rate of pregnancy, and increase the rate of implantation as well as decrease the chances of early pregnancy loss.

Effect of hepatitis C virus infection on the outcomes of in vitro fertilization.

look at this

PMID 26131230

The objective of this experiment was to investigate the effects that the Hepatitis C Virus (HCV) infection has upon the outcome In Vitro Fertilisation (IVF). From January 2008 - December 2013 a large sample of data was collected from couples opting for IVF at the Centre for Reproductive Medicine, General Hospital of Tianjin Medical University. These 1424 couples were tested for the HCV antibody (HCV-Ab) and were then separated into 3 groups. Group A contained 90 couples where the female tested HCV positive, Group B had 78 couples in which the male partner tested HCV positive and Group C - was the control group, of 1256 couples that both tested negative for HCV. The control group was also matched in age and in accordance with the IVF ovarian hyper stimulation protocol. These couples then underwent IVF and the results were closely monitored.

Initially the sperm was collected and its concentration, volume, motility, normal sperm morphology percentage (NMP) and Teratozoospermia index (TZI) were assessed, and again tested for the presence of HCV-Ab. The women were tested with Follicle Stimulating Hormone (FSH) on days 2-4 of their Menstrual cycle, within the 6 months of IVF treatment. They underwent Ovarian Hyperstilumation, and intramuscular injections of chronic Gonadotropin to mature the Oocytes. Transvaginal collection of mature Oocytes occurred roughly 36 hours later. 3 days later 2 high quality embryos were then transferred back into the uterus and oral progesterone was administered to support the Luteal phase of menstruation cycle. 14 days after the embryo transfer, pregnancy can be detected by testing for increasing levels of hCG in the blood, and can later, be clinically diagnosed through the presence of gastrointestinal sac during an abdominal ultrasound.

They found that all the groups (HVC positive male, HCV positive female , HCV negative couples) had similar results in terms of age, ovarian response, endometrial thickness, duration of Gonadotropin administration, embryo transfer and day of hCG administration, and no obvious differences within the sperm parameters; motility, concentration , PR differences, volume and NMP, TZI. They proceeded to investigate the effects of HCV on pregnancy and found no notable differences on pregnancy rates per cycle. They came to the conclusion that HVC had no effect upon IVF treatment or pregnancy.

--Mark Hill (talk) 10:36, 4 September 2015 (AEST)These are good summaries of the 2 papers. You did not need to keep "look at this " at the front of the reference code. (5/5)

Lab 2 Assessment

Upload a research image using the guide information below. The image uploaded for your individual assessment can relate to your project or from fertilisation to week 3 of development (upload only a single image).

Add that image to your own individual page (see Images) including an image title and its reference link.

Uploading Images in 5 Easy Steps

First Read the help page Images and Copyright Tutorial. Hint - This exercise is best done by using separate tabs on your browser so that you can keep all the relevant pages easily available. You can also use your own discussion page to copy and paste links, text. PMIDs etc that you will need in this process. Find an image . Search PubMed using an appropriate search term. Note that there is a special library of complete (full online) article and review texts called PubMed Central (PMC). Be very careful, while some of these PMC papers allow reuse, not all do and to add the reference link to your image you will still need to use the PMID. You can also make your own search term. In this link example PMC is searched for images related to "embryo+implantation" http://www.ncbi.nlm.nih.gov/pmc/?term=embryo+implantation&report=imagesdocsum. simply replace "embryo+implantation" with your own search term, but remember not everything in PMC can be reused, you will still need to find the "copyright notice" on the full paper, no notice, no reuse. Where else can I look? BioMed Central is a separate online database of journals that allow reuse of article content. Also look at the local page Journals that provides additional resources. You have found an image, go to step 2. Check the Copyright. I cannot emphasise enough the importance of this second step. The rule is unless there is an obvious copyright statement that clearly allows reuse (there are several different kinds of copyright, some do not) located in the article or on the article page, move on and find another resource. Not complying with this is a serious academic infringement equivalent to plagiarism."Plagiarism at UNSW is defined as using the words or ideas of others and passing them off as your own." (extract from UNSW statement on Academic Honesty and Plagiarism) You have found the statement and it allows reuse, go to step 3. Downloading your image. Download the image to your own computer. Either use the download image on the page or right click the image. To find the downloaded image you may have to look in your computer downloads folder, or the default location for downloaded files. The image file will have its own original name, that you will not be using on the wiki. You can rename it now (see renaming below), but you should also make a note of the original name. Make sure you have everything ready then for the You have the image file on your computer, go to step 4. Uploading your image. First make sure you have all the information you want to use with the file readily available. There is also a detailed description below. Towards the bottom of the lefthand menuunder “Toolbox” click Upload file. This will open a new window. In the top window "Source file", click "Choose file" and then navigate to find the file on the computer. and select the image. If you have done this correctly the upload window will now have your image file shown in choose file and also in the lower window "File description" in "Destination filename:" DO NOT CLICK UPLOAD FILE YET. Rename your file in "Destination filename:" this should be a brief filename that describes the image. Not any of the following - the original file name, image, file, my image, your ZID, etc. Many of the common embryology names may have already been used, but you can add a number (01, 02, 03, etc) or the PMID number to the filename to make it unique. If the filename or image has already been used or exists it will be shown on the upload page. If another student has already uploaded that image you will have to find another file. Duplicated images will not receive a mark, so check before you upload as you cannot delete images. In the "Summary" window for now just paste the PMID. You will come back and edit this information. Now click "Upload image" at the bottom of the window, go to step 4. Edit and Add to your page. Edit - Open the image with the "Edit" tab at the top of its page. You should see the PMID you had pasted earlier in the new edit window. Add the following information to the summary box. Image Title as a sub-heading. Under this title add the original figure legend or your own description of the image. Image Reference sub-sub-heading. Use the PMID link method shown in Lab 1 and you can also have a direct link to the original Journal article. Image Copyright sub-sub-heading. Add the copyright information under this sub-sub-heading exactly as shown in the original paper. Student Image template, as shown here {{Template:Student Image}} to show that it is a student uploaded image. Add - Now add your image to your own page under a subheading for Lab 2 Assessment including a description and a reference link. If still stuck with this last step, look at the example on the Test Student page. Done! Students cannot delete images once uploaded. You will need to email me with the full image name and request deletion, that I am happy to do with no penalty if done before I assess. Non-Table version of this page Stress Relief.... <html5media height="480" width="640">http://www.youtube.com/watch?v=i9Hwn2DOgKo</html5media>

look at this

PMID 26250560

Ovarian stem Cell Schematic

thumb

PMID 26250560

--Mark Hill (talk) 10:42, 4 September 2015 (AEST) Image uploaded correctly with reference, copyright and student template. The uploaded image size is so small the text cannot be read, you should have used a larger version of the original figure. Just a few minor issues. The Image title (Ovarian Structural scematic and stained cortical region of an ovariana stem cell .jpg) is far too long and includes an unnecessary space at the end. This could have been (Ovarian stem cell cartoon.jpg). Your subheadings have not been updated/formatted correctly and you have not formatted the reference correctly (I have fixed the reference this please see the difference). While all these are minor, it shows you are not reviewing your work. (4/5)

Lab 3 Assessment

In Lab 3 you were asked to divide the group project among your members and to research your allocated project component.

You will need to demonstrate that you have actively researched your project topic over the last week by having your section heading appear on the project page and have at least 3 research/review articles listed under that sub-heading.

The same content should be passed on your own individual assessment page.

Prenatal Diagnosis

Prenatal diagnosis is the screening process that tests an early fetus for overall growth, complications of pregnancy, birth defects and chromosomal or genetic abnormalities within the first 2 trimesters. It aims to provide the parents with as information as possible to help them make an informed decision about the infants quality of life. In 90-95% of the cases negative outcomes occur; confirming the healthy state of the fetus, should a genetic abnormality be present, it provides the parents with the opportunity to investigate further with other tests, and possible fetal therapeutic treatments available as well plan and prepare for the disabled infant or to terminate the pregnancy.

Post Implantation Genetic Diagnosis

• Indicators for prenatal screening/ high risk factors include:
  • maternal ages > 35 years
  • paternal ages > 50-55
  • history of 2+ miscarriages
  • previous pregnancy or family history of a preexisting genetic or chromosomal disorder
  • suspected carriers of genetic disorders
  • maternal disease/condition present (high BP, diabetes)
  • abnormal ultrasound or serum test results within the first 2 trimesters
  • family history of neural tube or other birth defects

• Ultrasonography:
  • high frequency sound waves are used to generate a image of the fetus
  • relatively non-invasion; its conducted transabdominally or transvaginally ( producing a higher resolution image)
  • It reveals the presence/absence of congenital abnormalities, characteristics of fetal growth and development, uterine development status; amount of **amniotic fluid, placental position, umbilical blood flow and the presence of multiple gestation.
  • (if abnormalities are detected further testing is recommended)

• Amniotic Fluid Analysis/:
  • samples are obtained through amniocentesis
  • the amniotic fluid is analyzed for its biochemical composition
  • earlier in the pregnancy it can be examined for sex determination and to diagnose genetic or chromosomal disorders present.
  • Later into the pregnancy it provides an indication of fetal maturity and well being
  • Feta; cells recovered from the amniotic fluid can be cultured for specific karyotypes, to test for Chromosomal Abnormalities, and analysed for Alpha- fetoprotein (AFP) a biochemical marker of metabolic disorders and neural tube defects as well as other abnormalities.
  • Amniocentesis- occurs usually between weeks 14-20 as amniotic fluid has reached the optimal volume (150-250mls) allowing 20-30mls to be removed with a relatively low risk or fetal or maternal complication, and in time for a 2nd trimester abortion.
  • early amniocentesis ( before week 13) increase the risk of fetal loss, leakage of essential amniotic fluid and talipes equinovarus.

• Chronic Villus Sampling (CVS):
  • occurs roughly 10-13 weeks after last menstrual cycle, ensuing a sufficiently developed chorionic villi but before the chorion laeve forms the definitive placenta.
  • ultrasounds is used to locate the gestational sac and implantation then a transcervial or transabdominal approach is used to aspirate living tropoblast tissue.
  • sample is analyzed for chromosomal abnormalities or with enzyme assay.
  • advantages: earlier diagnosis , decreased waiting period
  • disadvantages: risk of spontaneous abortion, bacterial infection, bleeding, leakage of amniotic fluid, inability to diagnose neural tube defects this early, early cleavage (before wk 10) is associated with increased risk of limb defects (due to insufficiently developed chronic villi)

• Umbilical Blood Sampling:
  • can occur as early as 16 weeks
  • using the umbilical cord to obtain fetal blood samples - with real time ultrasound
  • used to diagnose inherited blood disorders, to detect congenital infections, to assess fetal anemia and in treatments such as blood transfusions.
  • disadvantages: risks of infection, preterm labor, thrombosis, bleeding & transient fetal arrhythmia

• Fluroscent in Situ Hybridisation (FISH)
  • rapidly detects (within 24 hours of testing ) the presence of Trisomies 21, 13 and 8 and alterations in sex chromosomes in uncultured cells.

fetal therapies

early diagnosis allows the opportunity for intervention:

• surgical intervention urinary tract obstruction ; aiming to reduce prenatal renal damage
• fetal transfusions ( feta anemia
• fetal medical treatmetn ( fetal cardiac arrhythmias,impaired thyroid function etc.) treatment occurs usually through the mother
• infusions for hematologic conditions
• stem cell transplantation
• gene therapy
• pharmocolic interventions

textbooks used :

• Maternal, Fetal & Neonatal physiology: a Clinical perspective

• Langman's Medical Embryology (12th ed.)Chapter 9, pages 125-129

the following are two articles about a newly available and accessible prenatal non- invasive genetic test- Blood sampling:

• Report on Cutting edge prenatal screening technology to become available in Australia

• Blood Test takes risk out of prenatal testing

• Prenatal screening and Diagnostic Tests Information Pamphlet

<pubmed>26168107</pubmed>

--Mark Hill (talk) 10:46, 4 September 2015 (AEST) While you have included a lot of content for your group project, I only see a single PubMed reference here? The other sources are useful, but begin with the research literature. (4/5)

Lab 4 Assessment

ANAT2341 Quiz Example | Category:Quiz | ANAT2341 Student 2015 Quiz Questions |

Design 3 quiz questions based upon any of the major subjects we have covered to date. Add the quiz to your own page under Lab 4 assessment and provide a sub-sub-heading on the topic of the quiz. An example is shown below (open this page in view code or edit mode).

Gamatogenesis

Fertilisation and gamatogenesis

Spermatogenesis

ANAT2341 Lab 1 - Gametogenesis

1 { Which is the most correct statement about male Gamatogenesis :

	the entire process is driven by the secretions of the sertoli cells
	it does not occur before puberty
	meiosis is initiated by meitoically dividing stem cells
	it takes a males spermatozoa 38 hours from commencing meiosis until it reaches a mature spermtozoa.
	sperm does does not reach full maturity until fertilization.

2 The most correct sequence of spermatogenesis ( male gamatogenesis ) is:

	spermatozoa, spermatodytes, spermatid, spermatagonia
	sertoli cells, spermatocytes, spermatagonia, spermatozoa
	spermatogonia, spermatocytes, spermatids, spermatozoa
	spermatocytes, spermatids, spermatogonia, spermatozoa

3 Which of the following statements about gamatogenesis are True:

• A) Oogenesis enter arrest at the 1st meiotic stage and spermatogenesis does not enter arrest
• B) Meiosis is initiated twice in a finite population of cells
• C) Spermatogenesis produces 4 gametes/meiosis whereas oogenesis produces 1 gamete/meiosis
• D) In Oogenesis gamate differentiation occurs at the diploid phase and spermatogenesis it occurs in the haploid phase.

	none of the above
	A and C
	A,B,D
	A,C,D
	all of the above

- neither gamate has reached its full maturity when it leaves the gonad - spermatogenesis can not occur untill puberty and oogenesis is reactivated at puberty due to hormual stimulation from the endocrine system

fertilisation

Here are some further questions on fertilisation and Gamatogenesis Quiz 1

--Mark Hill (talk) 10:51, 4 September 2015 (AEST) These are indeed some thought provoking questions you have devised here. You could also have included links to pages where the student could read more about the topics. (9/10)

ANAT2341 Student 2015 Quiz Questions

Lab 5 Assessment

Select one of the topics shown below and write 3 paragraphs (with referenced sources) on that specific topic.

Cleft Lip and cleft palate are associated with many different environmental and genetic causes. Identify and describe one cause of these abnormalities.

Discuss how aganglionic colon is a gastrointestinal tract abnormality related to neural crest migration.

What is the difference between gastroschisis and omphalocele?

During regular embryonic development, the mid gut herniates the abdominal wall (week 6) and develops externally in a sac, ventral to the body wall (week 6-10). Once the fetus has grown to such a caliber that it is large enough and strong enough it recaptures the mid gut through the umbilical ring (week 11), it then rotates internally to reach its correct adult anatomical position. The midgut herniation is a possible site for abnormalities like Gastroschisis or Omphalocele to occur, due to congenital defects of the abdominal wall or abnormal rotation and fixation of the midgut.

Gastroschisis which is the abnormality where the herniated abdominal viscera (midgut) sit to the right of the intact umbilical cord on the outer anterior surface of the body wall, with no membranous covering, the viscera is susceptible to organ damage as it is directly exposed with the amniotic fluid. Although these are not abnormalities of the gastrointestinal system, it has a direct effect upon the development and functions of the GIT causing inflammation of the bowel and delayed alimentation. There are 2.5 cases/10,000 births, which is increasing incidence . Gastroschisis usually occurs in isolation but can be associated associated with young maternal age (< 20 years), folic acid deficiency as well as low gravida, prematurity, and low birth-weight babies, secondary to in utero growth retardation; fetal, Gastrointestinal anomalies (intestinal atresia, perforation, necrosis or volvulus), Hirschsprung's disease, Intestinal Atresia, GERD, Cryptorchidism and sporadically Oromandibular limb hypogenesis. Complications include resulting defects in other organs in 35% of cases and fetal distress. There are several possible theories explaining the cause of this abnormality; when the yolk sac and asscoiated vitelline structures are not included in the umbilical stalk, , due to a compromise in the vasculature of the right abdominal wall. Gastroschisis can be simply detected using ultrasound scan and has a relatively high mortality rate of 40%.

The Omphalocele, like Gastroschisis is an abnormailty that is caused by a congenital defect of the abdonminal wall,when the mid herniates the abdominal cavity, unlike the herniated Gastroschisis, the viscera is contained within the umbilical cord (unless it ruptures) and the organs are protected from the amniotic cavity. It is caused by a failure to recapture the herniated midgut in week 11. As long as the herniation is enclosed within a membrane (unless perforated) the midgut should develop and function normally. This condition does occur in association with increased maternal age, twins, consecutive children and different generations of the same family and as a result of with as a result of chromosomal disorders (25-50 % of cases) trisomy 13,14,14,18,21 and also with Beckwith-Wiedemann Syndrome, Macrosomia, GERD Cryptorchidism Musculoskeletal Neural tube defects and congenital heart defects.. Omphalocele and Ganstroschisis are similar conditions with a few essential points of difference.

summary:

Gastroschisis:

Not covered by membrane directly impacts GIT function impaired GIT function herniation lies to the right of umbilical cord occurs isolation and less often with associated conditions higher risk of complication Lower mortality rate, 60% survival rate Larger rate of incidence Unsure of origin- there are several theories easy prenatal diagnosis variable postnatal outcomes.

omphalocele'

Covered by membrane indirectly impacts GIT normal GIT function Herniation within umbilical cord linked with chrosomal abnormalities and other conditions Trisomy 13,14,14,18,21 Higher risk of complication originates in failure to retract the loops of midgut

Lab 6 assessment

History

Historically prenatal genetic diagnosis were conducted post-implantation in the first 2 trimesters, testing for overall fetal growth, complications of pregnancy, birth defects and chromosomal or genetic abnormalities, although, currently these genetic tests are conducted as a part of PreImplantation Genetic Diagnosis (PGD) made possible by the recent advances in Assisted Reproductive Technologies (ART).

Genetic Techniques

main indicaators of the presence single gene disorders (PCR) and inherited chromosome abnormalities(FISH) PMID 25154779 (might be useful?)

Fluorescent In Situ Hybridisation (FISH)

Fluorescence in situ hybridization (FISH) the one of the most effective and rapid Preimplantation Genetic Diagnosis (PGD) techniques used to locate specific DNA sequences within a chromosome. FISH facilitates the clinical diagnosis of chromosomal abnormalities indicated by sequential duplications, deletions and rearrangements of chromosome, which are usually missed with microscopic analysis. This technique is especially relevant for female embryos with X-linked diseases, that have no other mutation specific tests. (http://www.ncbi.nlm.nih.gov/pubmed/20809319) As part of PGD samples are collected from various stages of the embyro, with the test being conducted on the blastocyst, polar body biopsy and blastomeres. FISH is 99% effective when used in conjunction with competitive Genomic Hybridisation (CGH) in diagnosing chromosomal abnormalities.

How does it work ? Probes are short single strands of DNA that have been tagged with fluorescent labels to complement specific parts of each chromosome. These probes are usually target specific or used in a specific combination to test for specific loci. These fluorescent labels are small chemical agents that glow brightly in the presence of a specific region on a chromosome. Heating the DNA sample denatures it, causing the individual DNA strands to break apart, allowing the probe to hybridise (join with) the complementary strand of DNA. the fluorescent tags enable the researchers to correctly identify the presence or lack thereof and location of the specific chromosomes that they are testing for. The probe will not hybridise is the there has been a duplication or a deletion of the DNA - indicating chromosomal abnormalities such as trisomies 13,18 and 21

PMID: 26338801 PMID: 11325751 PMID: PMID: 11325751 PMC1120169 PMID: 17970921

Unique, Rare Chromosome Disorder Support Group (2013) Fluorescence in situ hybridisation (FISH) Rarechromo.org retrieved from [23]

NIS (2015) Flourescence in Situ Hydridization (FISH) National Human Genome Research Institute retrieved from [24]

Lab 7 assessment

1. Identify and write a brief description of the findings of a recent research paper on development of one of the endocrine organs covered in today's practical.

Proteomic characterization of adrenal gland embryonic development reveals early initiation of steroid metabolism and reduction of the retinoic acid pathway.

The molecular mechanism of adrenal Gland development are not well understood or documented. The purpose of this study was to identify the protein pathways that initiate the specification of the endocrine function in the adrenal gland and provide a comprehensive proteome analysis for 3 separate stages. Electrophoresis ad mass spectrometry analysis were use to monitor the alterations of proteome on at embryonic days (E) E16 and E19 and post natal day 1 P1. They found that the key proteins of cholesterol synthesis increased expression significantly at E19 showing the initiation of endocrine specialization and, that retinoic acid pathways decreased during adrenal gland development , possibly indicating its role in the early stage development.

(More ? Adrenal Development )

2. Identify the embryonic layers and tissues that contribute to the developing teeth.

Odontogenesis or tooth development initiates in week 6 of embryonic development and is contributed to the following cells and tissue layers:

Odontoblasts: are ectomesenchyme cells derived from the neurocrest,. They initially form predentin that calcifies to form dentin, this dentogenesis is driven by the influence of enamel epithelium. (week14)

Ameloblasts: are a derivative of epithelium from the ectoderm cells of the first pharyngeal arch. They produce enamel which covers the crown of the tooth, and are only present during odotogenesis. (week 14)

Peridontal Ligament is a specialized connective tissue containing Shapey's Fibres (specialized collagen fibre bundles) that holds the tooth in place in its socket. It functions as a shock absorber transmitting the chewing forces , as well as relays sensory information like heat, cold, pain and pressure.

Odontogenesis has 4 key stages: bud (week 8), cap (week 11), bell (Week 14) and terminal differentiation.

(Tooth Development UNSW embryology)

<pubmed> 18671204 </pubmed>

History

Prenatal Genetic Diagnosis was historically conducted post-implantation in the first 2 trimesters , testing for overall fetal growth, complications of pregnancy, birth defects as well as chromosomal or genetic abnormalities. Due to advancements in Artificial Reproductive Technologies ( ART) in the past 2 decades , these genetic tests are now conducted as a part of Preimplantation Genetic Diagnosis (PGD) and art used to eliminate the rsik of passing on a genetic disorder to an offspring, before implantation, it ha now become a preventative measure. . In 1990 Preimplantation genetic testing was first used in 1990 on humans to diagnose recessive X-linked diseases in the embryos of pregnant women undergoing IVF. PGD is offered as an alternative to prenatal diagnosis in detecting genetic disorders in high risk couples and avoid passing an inherited disease to the offspring, by selecting genetically "normal" embryos for implantation ,to give the best chance of successful implantation , stable pregnancies and healthy children.

Genetic Techniques

PCR

Description

Polymerase chain reaction (PCR) amplifies DNA specific to genetic sequence of interest . PCR was developed by Kay Mullis in the 1980s, for which he was awarded the Nobel prize for chemistry in 1993. This technique enables clinicians to monitor and diagnose diseases using minute samples such as embryonic cells, blood & tissue. PCR has many important applications like DNA fingerprinting, genetic mapping, detection of viruses and bacteria as well as being used to detect genetic disorders, as a part of PGD, in conjunction with IVF. It is used to detect molecular abnormalities such as single gene disorders like Tay Sach, Cycstic fibrosis, Duchenne Muscular Dystrophy, Thalassemia, Huntington disease, Spinal muscular atrophy and many more. Molecular and Genetic analysis require a significant amount of DNA, which we would not have without PCR. It revolutionized the study of DNA, replacing all previous recombinant DNA technology.

Procedure

Sample are obtained from the the blastocyst, a polar body biopsy or the blastomeres stages of the embryo. Stage 1 Denaturing: separating the target strands of DNA The obtained sample is heated to roughly 90 degrees celcius, this heat causes breaks the relatively weak bonds between nucleotides that form DNA. the double stranded DNA to split into 2 single strands of DNA that are used as templates. Stage 2 Annealing: Binding the Primers to the target DNA sequence PCR will only copy the target sequence of DNA specified by specific PCR primer. These synthesized primers Oligonucleotides are small artificial pieces of DNA. TAQ polymerase enzyme synthesize 2 new strands of DNA duplicate to the single sample DNA stand template indicated by these primers. During this stage the reaction is cooled to a temperature between 40-60 degrees Celsius. Stage 3- Extension- making copies Each of these 2 copies are then used again as templates generating 2 further replications This cycle can occur as many 30 -40 times within a couple hours leading to billions of extra copies of the original DNA segment. The optimal temperature for the further replication is roughly 72 degrees Celsius.

PCR Cycle	Target Copies
1	2
2	4
3	8
4	16
5	32
6	64
7	128
8	256
9	512
10	1024
15	32,768
20	1,048,578
25	33,554,432
30	1,073,741,842

This process mediated by a thermocycler machine that is programmed to alter the temperature of the reaction every couple of minutes, perpetuating the cycle of DNA denaturing and synthesis. This process, generates exponential exact copy of the original template DNA sequence.

Advantages & Disadvantages

ADVANTAGES

• fast and inexpensive way of copying a target sequence of DNA
• aids the diagnosis of single cell defects
• rapid generation of results within a couple hours
• can start from a single molecule of DNA, therefore is more sensitive
• has a flexible primer design enabling
• overcame previous issues associated with the limited availability of sites of end
• generates the DNA copies exponentially
• enables DNA amplification required for molecular and genetic analysis
• Valid diagnostic method in selecting unaffected embryos for embryo transfer

DISADVANTAGES

• only during this exponential DNA replication phase can we determine the starting quantity sequence contained in the original sample ( template DNA strand)
• PCR reaction is limited by the presence of inhibitors present in the sample :

reagent inhibitors

• self annealing due to the accumulation of the product -stopping exponential amplification for the target sequence and reach a plateau

quantification of the end point of reaction of PCR products unreliable - therefore that is why we require real time quantitative RT-PCR necessary

Fluorescent In Situ Hybridisation (FISH)

Description

Fluorescence in situ hybridization (FISH) the one of the most effective and rapid Preimplantation Genetic Diagnosis (PGD). This techniques used to locate a specific DNA sequences within a chromosome. FISH facilitates the clinical diagnosis of chromosomal abnormalities indicated by sequential duplications, deletions and rearrangements of chromosome, that are usually missed with microscopic analysis. This technique is especially relevant for female embryos with X-linked diseases, that have no other mutation specific tests [25] As part of PGD, samples are collected from various stages of the embyro,and they are able to conducted tests on the blastocyst, a polar body biopsy and the blastomeres . FISH is 99% effective when used in conjunction with competitive Genomic Hybridisation (CGH) to diagnose chromosomal abnormalities.

Procedure

Samples are collected from either the blastocyst, a polar body biopsy or the blastomeres stages of the embryo . DNA strands are heated and denatured causing their the individual DNA strands to break apart Probes are single complimentary stands of DNA a that have been tagged with small chemical agents that glow brightly in the presence of a specific region on a chromosome. These specific probes then hybridize and join to their complementary DNA strand. The fluorescent tags enable the researchers to correctly identify the presence or lack thereof and location of the specific chromosomes that they are testing for. Researcher analyse the results by identifying the number and the relative location of the fluorescent dots generated by the FISH images. The probe will not fully hybridise if there has been a duplication or a deletion of the DNA - indicating chromosomal and sex chromosomal anomalies like trisomies and aneuploidies.

Different probes are used for different purposes:

• Locus specific tags detect very small imbalances, and locate isolated small portions

of genes within a chromosome

• Alphoid/Centomeric Repeat probes are developed from the repetitive sequence located in the middle region of each chromosome, useful in determining the number of chromosomes , detecting rearrangement and when used in conjunction with locus probes to determine the absence of genetic material on a chromosome.
• Paint Probes are collections of smaller probes with their own stains that bind to a different section on the chromosome - allowing the full chromosome too be labeled a unique colour, this "full colour map" can be used to know the spectral karyotype- full chromosomal mapping is useful in examining chromosomal abnormalities.

Advantages & Disadvantages

ADVANTAGES

• FISH is 99% effective when used in conjunction with Competitive Genomic Hybridisation (CGH) to diagnose chromosomal abnormalities.
• rapid generation of results
• enables the number and size of specific chromosomes to be known
• identifies very small translocations and aneuploidies that occur within chromosomes, that would usually be missed under microscopic analysis
• indicates whether the accessed chromosomes are normal
• tests for the most common chromosomal abnormalities - down syndrome chromosomes 13,16,18,21 and 22
• can be used to identify and remove inheritable X-linked disease or sex chromasome anomalies such as Duchennes Muscular Dystrophy, hemophilia, ectodermal dysplasia
• it may be used to compare the chromosomal gene arrangements in related species

DISADVANTAGES

• FISH destroys all cells tested
• it does not fully access all chromosomes ( only ~ 12),
• there is a 40 % chance that chromosomal aneuploidy is occuring and not being targeted by this test
• analysis of results is dependent upon the dot quality impacted by hybridisation efficiency or the camera sensitivity
• some studies indicate that using FISH on a day-3 embryo biopsy decreases the rate of live births

PMID 11325751

Array Comparative Genomic Hybridisation (aCGH)

Description

aCGH also known as Microarray analysis efficiently scans the entire genome for chromosomal imbalances. CGH was initially developed to detect the number of changes in a solid tumor mass. It uses 2 genomes comparing the sample to the control, with each labeled in a different fluorescent dye. Earlier CGH techniques were limited by the resolution of the imaging , these initial limitations were overcome by using Microarrays in conjunction with CGh to improve the resolution of the imaging, Array Comparative Genomic Hybridisation (aCGH). This method compares sample and control microarrayed slides containing small segments of DNA (probes). the Probes used will vary according from the small (25-85 base pairs) oligonucleotides manufactured to highlight different target sequences, to the very large genomic clones (80,000- 200,00 base pairs), and as these are significantly smaller than the traditional metaphase chromosomes used for CGH, generating a higher resolution of image. .aCGH is used as a diagnostic tool for prenatal detection f chromosomal abnormalities .

Procedure

• sample is obtained (skin, blood or fetal cells) and DNA is obtained.

As a part of PGD fetal cell samples are collected from; the fertilized egg polar bodies, the blastomere (day 3 embryo) or the blastocyst/tropoectoderm stage (day 5 embryo).

• Sample DNA is labeled with one fluorescent dye, and the control DNA is labeled with a different colored fluorescent dye. the control DNA is used as the base point of reference.

heated and denatured single DNA strands then hybridize to their complementary single strand probes

• these are then combined and applied to a microarray
• the results are run through a computer program and a digital imaging system is used to quantify the results( fluorescent intensities of the labeled probes).

simple explanation of aCGH : [Genomics Education (2014) Genetic Testing for Health: aCGH|https://vimeo.com/84757281]

The fluorescent ratio and the hybridization signal at different locations on the genome of the control DNA are used to identify any variances present in the sample DNA,. aCGH facilitates the clinical diagnosis of submicroscopic chromosomal duplication, deletion and rearrangements indicative of chromosomal disorders such as trisomies 1-22and specific sex linked disorders. Duplications in the DNA are displayed by the computer program as spikes/ peaks over an established threshold and deletions in DNA are displayed by the computer program as spikes/ toughs beneath this threshold -computer screening image- -drawn diagram of method-

Advantages & Disadvantages

ADVANTAGES:

• multiple applications: prenatal genetic diagnosis, cancer diagnosis, genetic screening for developmental delay (learning disabilities) . or congenital anomalies that are suspected to be genetic in origin
• trace represents all chromosomes present in the human genome chromosomes 1-22 and the X & Y chromosomes, and therefore is the most accurate method for testing whole embryo aneuploidy
• aCGH has been extensively tested, and Validated, and is now used world wide.
• detects deletions and additions and rearrangements as well as amplification, of the WHOLE genome, simultaneously.
• detects submicroscopic alterations
• used as a diagnostic tool for prenatal detection of chromosomal abnormalities .

• provides high resolution genomewide screening of segmental genomic copy number variations
• very accurate when used in conjunction with FISH
• Alone is more reliable and in detecting chromosomal abnormalities, with a higher implantation success rate, than FISH .
• Allows an in depth research focus upon specific types of rearrangements within selected chromosomal regions, a recent particular area of interest is subtelomeric and pericentromeric rearrangements
• reduces the risk of failed implantation and miscarriage, improving the chance of a healthy baby

DISADVANTAGES:

• translocations and inversions of DNA are not detected
• limited ability diagnosing specific polyploidies such as triploidy
• will not detect mosaicism detection <20% (cultures where >1 of 5 cells are trisomy 12)
• will not detect balanced chromosomal rearrangement
• will not detect duplications or deletions <80kb
• will not detect point mutations within genes
• will not detect chromosomal position of genomic gains
• will not detect loos of heterozygosity (LOH) or Absence of heterozygosity (AOH)

Next Generation Sequencing

Description

The development and advances within ART in the past 20 years, as well as the increasing popularity of IV, has lead to an influx of new technologies developed to screen embryos for chromosomal anomalies, which are covered by the umbrella term of Next generation Sequencing (NGS). NGS is a general term used to describe all of the new and emerging screening techniques currently being introduced and used as part of PGD for IVF . NGS screens for single gene disorders as well as conducting extensive and very comprehensive chromosome diagnosis by sequencing, counting, and accurately assembling millions of DNA reads, simultaneously. There is a movementfor NGS to replace the other limited testing techniques and be used as the standard.

Procedure

Samples are collected from either blastomere or the blastocyst/tropoectoderm and processed for analysis by a computer system. The methodology of each process is unique to the technique being used.

Advantages & Disadvantages

ADVANTAGES:

• cheaper
• opens new diagnostic possibilities
• accurately tests all 24 chromosomes
• tests for the presence of monogenic diseases of known genetic background
• reduces the number of biopsies required for diagnosis
• higher detection rate of small translocations
• highly accurate is testing for compound point mutations, chromosomal duplication, deletions and insertions
• it accurately detects chromosomal aneuploidy and unbalanced rearrangement
• NGS single gene disorder screenings can conducted in conjunction with PCR comprehensive chromosomal screening.
• Reduces human error
• better detects the presence of mosaicism
• work well in conjunction with CGH and aCGH as part of PGD, improving the chances of IVF.

DISADVANTAGES: there is limited information available to clinical applications of NGS

Lab Attendance

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References

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