Arrays/NGS/NIPD

Question 1

What are the advantages of prenatal arrays

Answer 1

No culturing: increase TaT, no culturing artefacts.

Higher detection rates

Question 2

What are the disadvantages to prenatal arrays

Answer 2

Poor DNA quality/quantity. Miss balanced rearr and triploidy. Lower mosaic diet pectin rate to karyotype. Culturing is still required (DNA extraction, FISH, K follow up). Difficult interpretation. Cost of aCGH (and possible FISH). VOUS detected. Counselling issues. Coverage vs optimum resolution.

Question 3

What measures can be put into place in terms of platform used to help with the processing, analysis, interpretation.

Answer 3

Use same platform as postnatal array.
Allows: analysts to have experience, interpretation is easier as have in house dataset for the platform with clinical features, and local common benign CNVs.

Question 4

What did Huang and Crolla 2010 say about increasing platform resolution

Answer 4

There’s growing evidence that the use of a higher density arrays leads to no increase in diagnostic utility but does lead to an increase in discovery of benign and uncertain CNVs.

Question 5

What to consider in a prenatal setting when array shows an inherited cnv

Answer 5

If the parent has a normal phenotype consider: autosomal recessive condition in the region: other parent could be a carrier. Is the region imprinted. Does the region have a risk factor to disease- incomplete penetrance.

Question 6

What’s recommendations where published about prenatal arrays

Answer 6

RCPath recommendations for the use of chromosomal micro arrays in pregnancy June 2014

Question 7

What the RCPath criteria for using aCGH

Answer 7

One or more structural abnormality off scan.

Isolated NT of over 3.5mm with a crown rump length of 45-84mm.

Fetus with a sex chromosome abnormality that doesn’t explain the ultrasound.

Question 8

What’s the RCPath reporting rule for CNVs

Answer 8

Use 1-5 classification system

Report any variant that’ll potentially inform management of pregnancy/family now or in the future, regardless of size.

Question 9

What are the 3 examples of types of CNVs that the RCPath say SHOULD be reported

Answer 9

High penetrance neuro-susceptibility loci associated with a risk of severe phenotype (discussion about overall likely phenotype of the child).

Neuro-susceptibility locus associated with an increased incidence of anomalies detectable on scan (can direct further scanning).

Unsolicited pathogenic findings fulfilling the above criteria (deletion of known cancer predisposition gene-BRCA1. Deletion of DMD in a female fetus)

Question 10

What incidental findings ARE NOT reported by RCPath

Answer 10

Any finding:

Not linked to the potential phenotype for the pregnancy in question.

No clinically actionable consequence for the ciphers/family in the future.

VOUS that can’t be linked to phenotype based on genes involved.
Low penetrance neuro-susceptibility loci.
Unsolicited pathogenic variants where there’s no available intervention.

Question 11

What type of variants would be taken to the expert advisory group for prenatal CNVs

Answer 11

1) VOUS not on the reporting list.
2) Dups of known genes with poorly delineated phenotypes.
3) Del/dup of non-OMIM morbid genes.
4) Del/dup of AR genes tenuously linked to phenotype.
5) X-linked or recessive carrier status

Question 12

Who should be at the expert advisory groups for prenatal CNVs

Answer 12

2 clinical scientists and 2 clinical geneticists. Max TaT 2-3 days for a decision.

Written report to be provided/ reviewer to explain their decision. Collated/ recovered by date- to refer to in future cases.

Where possible feedback of pregnancy outcome given to the lab for inclusion in the review panel database .

Question 13

Which neuro-susceptibility loci SHOULD be reported

Answer 13

1) distal 1q21.1 deletion/duplication.
2) 15q13.3 deletion.
3) distal 16p11.2 deletion.
4) proximal 16p11.2 deletion.
5) 17q12 deletion.

Question 14

Which neuro-susceptibility loci SHOULD NOT be reported

Answer 14

1) 15q11.2 BP1-2 deletion /duplication.
2) 16p13.11 deletion/duplication.
3) proximal 1q21.1 duplication.
4) 16p12.2 deletion.
5) Xp22.31 (STS) duplication.
6) Xp22.33 (SHOX) deletion.

Question 15

Which neuro-susceptibility loci SHOULD BE CONSIDERED for reported

Answer 15

1) 22q11.2 duplication.
2) proximal 1q21.1 deletion.
3) 17q12 duplication.

Question 16

What percentage additional abnormalities did Hillman et Al 2011 say aCGH would provide to abnormal scans

Answer 16

5.2% increase after CNVs are removed

Question 17

What are the possible causes of error with NIPD

Answer 17

CPM.
Maternal chr rearr.
Maternal X/XX mosiciam.
Twin demise.
Maternal malignancy

Question 18

What test would you use to detect epigenetic changes in the 2 genes used

Answer 18

SERPINB5: (hypo) methylation specific PCR (bisulfite)

RASSF1: (hyper) methylation sensitive restriction enzyme digestion (cuts hypo- mat).

Question 19

What ad monogenic discerns are currently availed for NIPD

Answer 19

Achondroplasia. Huntingtons. Apert syndrome.

Question 20

How do you screen for a AR disorder by NIPD

Answer 20

If it’s a compound heterozygote: screen for paternal allele- if present- invasive test.

If it’s homozygous: use relative mutation dosage eg b-globin locus by digital PCR.

Question 21

What’s the PAGE study

Answer 21

Prenatal assessment of genomes and exomes.

Improve PND of fetal structural abnormalities by evaluating the role of WES/WGS.

Develop cost effective assays and catalysing adoption by the NHS.

Test 1000 trios by WES.

Isolated NT over 4mm / 1 or more structural anomaly.

Question 22

What’s the RAPID study

Answer 22

Reliable accurate prenatal non-invasive diagnosis.

Development of lab standards for NIPD of fetal sex determination/ monogenic disorders.

Comprehensive large scale evaluation of methods reported for NIPT for anueploidy (women with a risk of greater than 1:1000 are offered NIPT)

Question 23

What’s an outcome of these large scale study’s looking at fetal anomalies either by aCGH or WES/WGS

Answer 23

Number of known genetic variants likely to cause fetal anomalies will increase and with a detailed database eg DECIPHER, their clinical significance should become clearer.

Question 24

What general things need to be considered when assessing the use of NIPT

Answer 24

The uptake of NIPT by women.
How apt he addition of NIPT affects uptake to invasive tests and screening.
Barriers and facilitators.
Health economics.
Education of staff and public.
Sensitivity, specificity, positive predictive values.

Question 25

Name some different NIPT companies

Answer 25

Ariosa (harmony): agreed DANSR.

Illumina (Verinata): WGS: dosage.

Panorama (Natera): targeted 19,488 SNPs- compares SNPs from mat lymphocytes/ pat/ mat plasma cfDNA to work out relative copy numbers.

Question 26

What is preimplantation genetic diagnosis

Answer 26

The practice of obtaining a cellular biopsy sample obtained via a cycle of IVF, evaluating its genetic content to determine whether the embryo is suitable for uterine transfer.

Question 27

What are the mandatory NHS criteria for PGD

Answer 27

Clinical commissioning policy for 2014.

Reduce variation in access to PGD.
Commission PGD for conditions where there’s acceptable evidence of clinical benefit and cost effectiveness.
Promote cost effectiveness use of healthcare resources.

Question 28

For couples seeking PGD what are the criteria they have to achieve.

Answer 28

At risk of having a child with a serious genetic condition.
Been referred from clinical genetics/ have had counselling.
The risk of an affected pregnancy over 10%.
Women less than 40 yrs and BMI between 19-30.
Non smokers.
No unaffected children.
HFEA licenced the disease for PGD.
On UKGTN database.
Couple not seeking PGD because they’re infertile.

Question 29

What type of cells can be tested for PGD

Answer 29

1st and 2nd polar bodies.
Blastomeres (most common) 1-2 cells at day 3.
Blastocyst 10-30 cells at day 5.
Blastocentosis in development.

Question 30

What diseases are being tested for in PGD

Answer 30

Sex determination (X-linked disorder).
CF: 1st monogenic disorder.
Huntingtons: top AD disorder.
Mitochondrial disease (select embryos with lower number of mutated mtDNA)

Question 31

What ethical issues are there with PGD

Answer 31

HLA testing (BMT for sibling).

Selective transfer over selective abortion.
Risks to women undertaking procedure.
Designer babies.
Testing of late onset disorders.
Incomplete penetrance (BRCA1/2).

Couple who want to select for deafness.
Couples with achondroplasia who don’t want a homozygous, but don’t mind w. Or w.out achondroplasia.
Africa: sickle cell anaemia

Question 32

Name to disorder covered using NIPT fgfr3 panel

Answer 32

29 mutations

Achondroplasia. Thanatrophic dysplasia.