Divya Kalra

Project Personnel, Baylor College of Medicine

2 active projects

Assessing pathogenic variants in recessive genes v7

Genetic carriers are asymptomatic individuals with one copy of a mutation in genes with recessive inheritance. It is important to understand these carrier mutations as probands of such individuals have a higher chance of developing a recessive disorder, if both…

Scientific Questions Being Studied

Genetic carriers are asymptomatic individuals with one copy of a mutation in genes with recessive inheritance. It is important to understand these carrier mutations as probands of such individuals have a higher chance of developing a recessive disorder, if both parents are carriers of the same mutation. The All of Us (AoU) Research Program cohort will be used to assess the frequency of such events across genetic ancestry groups.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We plan to subset the genomic data to recessive genes and extract pathogenic/likely pathogenic variants based on ClinVar classification for further analysis. We also plan to filter variants for genes with LoF mechanism and do further analysis.

Anticipated Findings

We anticipate observing different rates of variants in such recessive genes across genetic ancestry groups. Analyzing these rates across ancestries would be very useful.

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Divya Kalra - Project Personnel, Baylor College of Medicine

Collaborators:

  • Eric Venner - Early Career Tenure-track Researcher, Baylor College of Medicine

vus-control

Variants of unknown significance (VUS) remain a challenge for genomic medicine as they are hard to interpret in clinical settings. We aim to extend existing workbench tools to allow for prioritizing of VUS as well as to extend our previous…

Scientific Questions Being Studied

Variants of unknown significance (VUS) remain a challenge for genomic medicine as they are hard to interpret in clinical settings. We aim to extend existing workbench tools to allow for prioritizing of VUS as well as to extend our previous work on pathogenic variants to include VUS and incorporate phenotype information, in the form of EMR codes and survey responses.

Project Purpose(s)

  • Ancestry

Scientific Approaches

We will build a Hail matrix table that annotates AoURP participants in the researcher workbench with their associated SNOMED codes and linked HPO terms via UMLS. We will then create a list of genes of interest by using HPO terms and deploy a Neptune (a previously developed platform for delivering clinical reporting) module that can work with these gene lists as input and prioritize variants in those genes, taking into consideration other available annotations that bear on pathogenicity.
We will then use this tool along with other workbench annotation resources to describe the genomic variant data available on the researcher workbench, and to select a small subset of variants that, when paired with case/control data taken from the EMR, are strong candidates for VUS reclassification, either as Pathogenic/Likely Pathogenic or Benign/Likely Benign.

Anticipated Findings

We anticipate having a new tool available on the workbench for others to prioritize potentially pathogenic variation for review and the new data resources that give the phenotype overlap between a participant’s SNOMED codes and genes

Demographic Categories of Interest

This study will not center on underrepresented populations.

Data Set Used

Controlled Tier

Research Team

Owner:

  • Yi-Ju Chen - Project Personnel, Baylor College of Medicine
  • Eric Venner - Early Career Tenure-track Researcher, Baylor College of Medicine
  • Divya Kalra - Project Personnel, Baylor College of Medicine

Collaborators:

  • Joshi Stephen - Early Career Tenure-track Researcher, Baylor College of Medicine
  • Aniko Sabo - Other, Baylor College of Medicine
  • Qiaoyan Wang - Project Personnel, Baylor College of Medicine
  • Lele Li - Project Personnel, Baylor College of Medicine
  • Kimberly Walker - Project Personnel, Baylor College of Medicine
  • Khalid Hakim - Project Personnel, Baylor College of Medicine
  • Bo Yuan - Other, Baylor College of Medicine
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