From Weitzman & NERGN Genetics Series. Recorded on April 12, 2021

1. Test Reports from Genetic and
Genomic Testing
Leah W. Burke, MD
April 12, 2021

2. Goals
• Review the parts of various genetic and
genomic testing results: Fragile X DNA,
microarray, genetic panels, exome
sequencing
• Demonstrate how the variants are
classified in the interpretation of results
• Use case reports to demonstrate how
more information can be obtained

3. Tier One Testing in Developmental
Delay/Autism Spectrum Disorder
• Fragile X DNA testing
• Chromosomal micrarray

4. Fragile X DNA Testing
• A trinucleotide repeat sequence syndrome
• Caused by an expanded (CGG) repeat
sequence in FMR1 gene at Xq28
• Must be tested for with a specific test that
determines the repeat size
• There will be two numbers of repeats for
females and one for males

8. Fragile X Syndrome
♀ ♂
5-44 Normal range Normal range
45-58 Intermediate zone Intermediate zone
59-200 Premutation Premutation
Over 200
Full mutation -
~50% affected
Full mutation -
100% affected
Repeat
Size

12. Analysis for
deletions or
duplications
SNP Analysis
for
LOH (loss of
heterozygosity
Normal
variants
REASON

17. Genetic vs Genomic
• Genetics and genomics both play roles in
health and disease
• Genetics refers to the study of genes and the
way that certain traits or conditions are
passed down from one generation to another
• Genomics describes the study of all of a
person's genes (the genome)
Genome.gov

18. Next Generation Sequencing
• A massively parallel sequencing technology in
which millions of overlapping “reads” of DNA
sequences are done simultaneously
• Creates an enormous amount of data to be
analyzed
• Can detect single gene pathogenic variants
including nonsense, missense, splice-site, and
frameshift variants
• Used in multiple gene panels as well as in
exome and genome sequencing
18

20. Classification of Variants
Pathogenic Alterations with sufficient evidence to
classify as pathogenic or capable of
causing disease Always reported
Likely Pathogenic Alterations with strong evidence in favor
of pathogenicity Always reported; may
suggest familial testing
Variant of Uncertain
Significance (VUS)
Alterations with limited and/or conflicting
evidence regarding pathogenicity
Often reported with suggestions for
further testing; depends upon lab
Likely Benign Alterations with strong evidence against
pathogenicity Often not reported in
results section but may be in
supplemental report
Benign Alterations with very strong evidence
against pathogenicity Not reported

23. Variants of Uncertain Significance (VUS)
• Insufficient or conflicting evidence to classify
as pathogenic or benign
• The variant classification changes over time as
more cases are reported
• May be reclassified with family testing
23

24. Case
• 3 month old
• Presented with seizures
• Some mild developmental delays
• No family history of epilepsy or seizures
• Epilepsy panel was sent

28. GeneReviews.org

29. GeneReviews.org

30. GeneReviews.org

31. Omim.org

32. https://medlineplus.gov/genetics/condition/slc
35a2-congenital-disorder-of-glycosylation/

33. Genetics Home Reference: Now on MedlinePlus

35. Summary of
Findings
Finding of a
VUS (variant
of uncertain
Significance)
Known benign
variant

36. Summary of
Findings
Finding of a
VUS (variant
of uncertain
Significance)
Known benign
variant

37. Classification of Variants
Pathogenic Alterations with sufficient evidence to
classify as pathogenic or capable of
causing disease Always reported
Likely Pathogenic Alterations with strong evidence in favor
of pathogenicity Always reported; may
suggest familial testing
Variant of Uncertain
Significance (VUS)
Alterations with limited and/or conflicting
evidence regarding pathogenicity
Often reported with suggestions for
further testing; depends upon lab
Likely Benign Alterations with strong evidence against
pathogenicity Often not reported in
results section but may be in
supplemental report
Benign Alterations with very strong evidence
against pathogenicity Not reported

38. Whole Genome and Exome
Sequencing

39. Whole Exome Sequencing
• Now being offered clinically
• Parallel sequencing of at least 98% of the
coding sequences
• Was recommended when all other diagnostic
testing has been negative
• Now being considered as a first line test for
sick NICU babies
• Recommend sequencing the child and both
parents together to address changes that are
not clear
39

40. NEJM Illustrated Glossary

41. Case
• 3 year old referred for developmental delay
and unusual physical features
• She had a microarray done that was normal
• Exome sequencing was done

44. Invitae.com

45. Invitae.com

46. OMIM: www.omim.org

48. From OMIM

50. Incidental Findings
• Findings unrelated to the question being
asked
• May have medical consequences that may not
be immediate
50

53. 53
March 2013
February 2017

54. ACMG- 2013 incidental Findings to
be reported
54

55. ACMG- 2016 Changes
55

56. ACMG Working Group Recommendations for
Reporting of Incidental Findings
56
When the exome or genome sequencing is done for clinical
indications:
• A minimum list of conditions, genes and variants should be routinely evaluated
and reported to the ordering clinician who can place them into the context of that
patient’s medical and family history, physical examination and other laboratory
testing
• These findings should be reported without seeking preferences from the patient
and family and without limitation due to the patient’s age
• This is an attempt to strike a balance between the positions of genetic libertarians
and the genetic empiricists, guided by the currently available scientific literature,
clinical experience, the consensus of our Working Group members and the
traditions of clinical medicine.
• This list should, and will, evolve as further empirical data are collected on the
actual penetrance of these variants, and on the health benefits and costs that
might follow from their disclosure as incidental findings

57. ACMG Working Group Recommendations for
Reporting of Incidental Findings
57
When the exome or genome sequencing is done for clinical
indications:
• A minimum list of conditions, genes and variants should be routinely evaluated
and reported to the ordering clinician who can place them into the context of that
patient’s medical and family history, physical examination and other laboratory
testing
• These findings should be reported without seeking preferences from the patient
and family and without limitation due to the patient’s age
• This is an attempt to strike a balance between the positions of genetic libertarians
and the genetic empiricists, guided by the currently available scientific literature,
clinical experience, the consensus of our Working Group members and the
traditions of clinical medicine.
• This list should, and will, evolve as further empirical data are collected on the
actual penetrance of these variants, and on the health benefits and costs that
might follow from their disclosure as incidental findings

58. Direct-to-consumer testing
58

59. Direct-to-Consumer (DTC) Genetic
Testing
• Advertised to the public
• Individuals order and receive
results directly from the company
• Mail in cheek swab or saliva
sample
• Typically use SNP array to detect
common SNPs in subset of genes
• No requirement for health
professional results interpretation
or pre-test counseling
59