Merging single gene-level CNV with sequence variant interpretation following the ACMGG/AMP sequence variant guidelines

Transcription

1 Merging single gene-level CNV with sequence variant interpretation following the ACMGG/AMP sequence variant guidelines Tracy Brandt, Ph.D., FACMG

2 Disclosure I am an employee of GeneDx, Inc., a wholly-owned subsidiary of OPKO Health, Inc.

3 ACMGG and AMP guidelines for interpretation of sequence variants Aims: Standardize terminology Guide for detailed, evidence-based classification Quantitative scoring system Pathogenic Evidence Benign Evidence Richards et al., Genetics in Medicine, (2015)

4 Richards et al., Genetics in Medicine, (2015) Tan et al., American Journal of Human Genetics, (2011) Example 1: pathogenic variant interpretation PTEN c.870dela in a patient with clinical dx of Cowden syndrome PVS1: Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) in a gene where LOF is a known mechanism of disease PM2: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium PP4: Patient s phenotype or family history is highly specific for a disease with a single genetic etiology Table 5 Rules for combining criteria to classify sequence variants = PATHOGENIC

5 Richards et al., Genetics in Medicine, (2015) Lek et al., Nature (2016) Example 2: likely benign variant interpretation NSD1 c A>G in a patient with overgrowth BS2: Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-Linked (hemizygous) disorder, with full penetrance expected at an early age BP4: Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.) = LIKELY BENIGN

6 Adaptation of guidelines for single-gene CNVs Per publication, To provide critical flexibility to variant classification, some criteria listed as one weight can be moved to another weight using professional judgment, depending on the evidence collected. the applicability and weight assigned to certain criteria may vary by gene and disease. Exon-level/gene-level CNVs mentioned only in PVS1 definition many criteria are directly applicable to single-gene CNVs others require minor adjustment

7 Challenges as we adapt criteria for CNVs Population databases are not as robust Exact break points are not always known, complicating CNV comparison Duplications are further complicated by unknown chromosomal location/orientation challenging to predict effect further complicating CNV comparison

8 Why adapt this classification system to CNVs affecting a single gene? Consistency A single test can produce sequence and copy number variants The same rules should be applied to classify/interpret both variant types Intra- and inter-laboratory consistency Convenience Analyst needs to interpret components from both results A single, powerful analysis/interpretation system is more efficient

9 Why adapt this classification system to CNVs affecting a single gene? As laboratories move towards a single method for both sequence variant and single-gene CNV detection, it becomes difficult to define/maintain boundaries between types of variants Reflective of this, ABMGG has merged cytogenetic and molecular genetic training into a combined LGG training program

10 Pathogenic criteria applicable to deletions involving one gene Previously established in-frame pathogenic deletion is entirely contained within in-frame deletion being evaluated and same disease mechanism is presumed Add CNV control databases, consider DGV with limitations Richards et al., Genetics in Medicine, (2015)

11 Benign criteria applicable to deletions involving one gene STAND ALONE CRITERIA BA1 STRONG CRITERIA BS1 BS2 BS4 SUPPORTING CRITERIA Allele frequency is >5% in ESP, 1000 Genomes Project, or ExAC Add CNV control databases, consider DGV with limitations Allele frequency is greater than expected for disorder Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age Lack of segregation in affected members of a family BP5 Variant found in a case with an alternate molecular basis for disease Richards et al., Genetics in Medicine, (2015)

12 Example 1: predicted null allele Evidence ACMGG/AMP criteria applied 5 end deletion including Met1 predicts null allele PVS1 Not in ClinVar, Decipher n/a DM in HGMD (publication reports female proband inherited deletion from affected n/a mother; however, lacks phenotypic details) Array probes No overlapping deletions in control cohorts If testing lab observes deletion in female w/ clinical diagnosis of craniofrontal nasal syndrome TOTAL PM2 PP4 PVS1+PM2+PP4 = pathogenic Twigg et al., American Journal of Human Genetics, (2006)

13 Example 2: in-frame deletion Evidence ACMGG/AMP criteria applied In-frame intragenic deletion PM4 Not in ClinVar, Decipher Deleted interval includes a critical domain No overlapping deletions in control cohorts If TOTAL completely contained, in-frame exon deletion was observed and classified as pathogenic TOTAL n/a PM1 PM2 SCN1A PM4+PM1+PM2 PS1 = likely pathogenic PM1+PM4+PM2+PS1= pathogenic Figure 1, Escayg et al., Epilepsia (2010) Nakayama et at al,. Human Mutation (2010)

14 Challenges in applying criteria Population databases not as robust - caution In-frame exon-level deletions, adjusted criteria required when applicable in-frame deletion of much of the coding region, not in controls, doesn t encompass critical domain PM4+PM2 = VUS gene-specific adjustment of PM4 to strong (PM4_strong) (e.g. DMD)? PM4_strong+PM2 = LPATH

15 Challenges in applying criteria - duplications! If break-points and orientation are known, criteria can be used more readily However, often we are not certain How can we apply criteria under these circumstances? Clinical criteria can be used Should we adjust existing criteria that are location/orientation dependent? Many criteria will not be applied, a duplication will often be classified as VUS

16 Next step, multigenic CNVs? ClinGen CNV interpretation guideline group- classification of multigenic CNVs Compatibility between all variant interpretation systems is important Using the same interpretation system will improve consistency is more convenient may be a better use of resources may prompt fields to evolve at same speed Increasingly difficult to define/maintain boundaries between types of variants More needs to be considered, but some of these criteria are applicable, such as inheritance/segregation based criteria criteria based on presence/absence from control samples

17 Summary The ACMGG/AMP sequence variant interpretation criteria describe an evidence-based scoring system aimed at increasing consistency/accuracy Many of these criteria are applicable to CNVs affecting a single gene Those that are not directly applicable can be adapted A single interpretation system for both sequence and copy number variants is critical to consistency and efficiency Collaboration across laboratories and freely-accessible tools to share variant data is imperative

18 Acknowledgements Jeanne Meck, Ph.D., FACMG Gabriele Richard, M.D., FACMG Dolores Arjona, Ph.D. Lisa Vincent, Ph.D., FACMG Caitlin Reavey, Ph.D. And many more GeneDx employees who worked to test, implement, and refine ACMGG/AMP criteria!