# Refining Mendelian disease analysis via detection of clinically relevant repeat variants

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2021 · $570,000

## Abstract

Project Summary
Next-generation sequencing (NGS) has the potential to profile all clinically relevant genetic variants simultane-
ously in a single genetic test. However, clinical variant discovery pipelines have mostly focused on coding single
nucleotide variants (SNVs), regulatory SNVs and small indels. This proposal aims to make repeat analysis a
standard component of existing pipelines, focusing in particular on short tandem repeats (STRs), variable number
tandem repeats (VNTRs), and low-copy repeats or segmental duplications. Together, these repeats account for
8% of the human genome, but are implicated in a disproportionately large number of Mendelian diseases. The
proposed methods are primarily aimed at Illumina sequencing, which forms the vast majority of current Mendelian
sequencing pipelines, but also includes alternative technologies such as Pacific Biosciences and 10X Genomics. The
first aim develops algorithms for discovery of repeat variants currently inaccessible from NGS. In the second aim,
the PIs propose to generate gold-standard validation data for Mendelian repeats using multiple technologies. In
the third aim, the PIs will integrate the proposed methods into existing NGS pipelines for clinical variant discov-
ery, and also apply them to large existing data-sets to obtain genotype frequencies of large control populations.
The project serves an unmet need by augmenting Mendelian variant pipelines to include highly relevant disease
variants.

## Key facts

- **NIH application ID:** 10205131
- **Project number:** 5R01HG010149-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Vineet Bafna
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $570,000
- **Award type:** 5
- **Project period:** 2018-09-14 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10205131

## Citation

> US National Institutes of Health, RePORTER application 10205131, Refining Mendelian disease analysis via detection of clinically relevant repeat variants (5R01HG010149-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10205131. Licensed CC0.

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