Case M arr [GRCh37] 16q22.1 - PowerPoint Presentation

Slide1

Case Marr[GRCh37] 16q22.1(68797032_68846703) x3

35-year-old male with gastric cancerAdditional studies have proven that the duplication is in tandem.

Note: These example CNVs have been created for educational purposes in order to ensure that each evidence type in the scoring matrices are utilized across the entire set (no single CNV will necessarily cover all evidence types).  These are not actual CNVs that have been observed in a laboratory setting.  As such, please evaluate the coordinates as given, regardless of other considerations that may apply in the actual clinical laboratory setting.  For example, if your CNV is below the size cutoff your laboratory uses on a daily basis, please disregard this for the sake of this exercise and evaluate the content within the provided coordinates. Assume that the CNV is technically valid.

Clinical Information

arr[GRCh37] 16q22.1 (68797032_68846703) x335-year-old male with gastric cancerAdditional studies have shown that the duplication is in tandem.Use the GAIN scoring metric

Section 1: Initial Assessment of Genomic Content

Would apply category 1A (contains protein-coding or other known functionally important elements), as this duplication includes several exons of a protein-coding gene.

0 points; continue evaluation

Total: 0 points

Case M

Section 2: Overlap with Established TS, HI, or Benign Genes/Genomic Regions

Case M

ClinGen Curated Track

CNV M is an intragenic duplication of a known HI gene,

CDH1

Use category 2I (both breakpoints are within the same HI gene, variant possibly resulting in LOF)

CDH1

Loss of function variants in CDH1 have been associated with hereditary diffuse gastric cancer (HDGC)Average age of onset: 38 years (range: 14-69 years)Majority of cancers in individuals with pathogenic variants in CDH1 occur before age 40

Estimated cumulative risk of gastric cancer by age 80 is 70% for men, 56% for women

Women also at risk for lobular breast cancer

Kaurah

P, Huntsman DG. Hereditary Diffuse Gastric Cancer. 2002 Nov 4 [Updated 2018 Mar 22]. In: Adam MP,

Ardinger

HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2020. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1139/

What is the predicted consequence of our duplication?

Abou

Tayoun

et al.

2018, PMID: 30192042

We know that additional studies have shown that CNV M is in tandem.

Need to assess the effect of this duplication on the reading frame.

Identify a biologically relevant transcript

For this example, we will use the MANE Select transcript.

Note that MANE transcripts use GRCh38 coordinates. We will need to lift over our GRCh37 coordinates.

Coordinate Remap from GRCh37 to GRCh38

Coordinate Remap from GRCh37 to GRCh38

GRCh37 coordinates

GRCh38 coordinates

Where do these coordinates fall within the gene?

There are multiple ways to determine this – here is one example (using Ensembl).

68763129 falls here

68812800 falls here

CNV M should include exons 3-8.

Is this in-frame or out-of-frame?

Add the total length of the missing exons

224 + 144 + 156 + 145 + 176 + 129 = 974

Is this number divisible by 3? Yes = In-frame; No = Out-of-frame

974/3 = 324.67

Not divisible by 3, predicted to disrupt reading frame

This gene has 16 exons total; this variant is not near the end of the gene, and would be expected to undergo NMD

PVS1 = 0.90 points

Total: 0.90 points

Section 3: Evaluation of Gene Number

CNV M is an intragenic duplication.

Use Category 3A, 0 points

Total: 0.90 points

Section 4: Detailed Evaluation of Genomic Content

When working with duplications that overlap TS, HI or Benign Genes/Genomic Regions (Section 2), you CAN use Section 4 to document additional evidence (and accumulate additional points) if you did not reach Benign or Pathogenic in Section 2.

If, for example, your CNV was a complete duplication of a known TS gene (Category 2A), using Section 4 would not be necessary.

If, for example, your CNV was a duplication with one breakpoint in a known HI gene associated with a highly specific phenotype (Category 2K) you may want to use Section 4 to identify other similar variants to use as evidence.

In our case (CNV M), we were able to get to Likely Pathogenic (0.90 points) in Section 2.

Option to use Section 4 to identify other literature cases of similar intragenic duplication variants in

CHD1

to get to Pathogenic

Option to use our patient’s consistent phenotype in Section 5 to get to Pathogenic

Will utilize this option for this example

Section 5: Evaluation of Inheritance Pattern/Family History for Patient Being Studied

Our patient is a 35-year-old man with gastric cancer

We were not told the specific pathology of the gastric cancer – do not know if it is diffuse gastric cancer

This is consistent with the expected phenotype, however, to be conservative (since we are not confident that this is diffuse gastric cancer), use Category 5G, 0.10 points.

Regardless of if we count this as non-specific or specific, we will still be able to add enough points to classify this variant as Pathogenic.

Total: 1.0 points

Conclusion

Classification: PathogenicThis duplication is predicted to disrupt the reading frame of a known HI gene. The patient’s phenotype is consistent with what is expected for Hereditary Diffuse Gastric Cancer.