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. 2019 May 17;11(1):30.
doi: 10.1186/s13073-019-0639-5.

Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

Avinash V Dharmadhikari  1 , Rajarshi Ghosh  2 , Bo Yuan  1   2 , Pengfei Liu  1   2 , Hongzheng Dai  1   2 , Sami Al Masri  1 , Jennifer Scull  1   2 , Jennifer E Posey  2 , Allen H Jiang  3 , Weimin He  1 , Francesco Vetrini  1 , Alicia A Braxton  1   2 , Patricia Ward  1   2 , Theodore Chiang  4 , Chunjing Qu  1 , Shen Gu  2 , Chad A Shaw  1   2 , Janice L Smith  1   2 , Seema Lalani  1   2 , Pawel Stankiewicz  1   2 , Sau-Wai Cheung  1   2 , Carlos A Bacino  2   5 , Ankita Patel  1   2 , Amy M Breman  1   2 , Xia Wang  1   2 , Linyan Meng  1   2 , Rui Xiao  1   2 , Fan Xia  1   2 , Donna Muzny  4 , Richard A Gibbs  2   4 , Arthur L Beaudet  2 , Christine M Eng  1   2 , James R Lupski  2   4   6   5 , Yaping Yang  1   2 , Weimin Bi  7   8
Affiliations

Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases

Avinash V Dharmadhikari et al. Genome Med. .

Abstract

Background: Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES.

Methods: In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array.

Results: The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities.

Conclusions: Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

Keywords: Dual molecular diagnoses; Exome sequencing; Exonic CNV in AR disorders; Microarray; ROH; Structural variation; Uniparental disomy.

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Conflict of interest statement

Baylor College of Medicine and Miraca Holdings Inc. have formed a joint venture with shared ownership and governance of Baylor Genetics (BG), formerly the Baylor Miraca Genetics Laboratories, which performs chromosomal microarray analysis and clinical exome sequencing. JRL serves on the Scientific Advisory Board of the BG. JRL has stock ownership in 23andMe, is a paid consultant for Regeneron Pharmaceuticals, and is a co-inventor on multiple US and European patents related to molecular diagnostics for inherited neuropathies, eye diseases, and bacterial genomic fingerprinting. Yang is a member of the Scientific Advisory Board (SAB) of Veritas Genetics China. The remaining authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Summary of PCNV/UPD findings from the quality control array and CMA. a A pie chart to show the types of aberrations detected by the QC array. b A table to show the proportion of patients with PCNVs/UPD from the QC array that were known or unknown prior to ES testing. c A pie chart to show the types of aberrations detected by CMA. d A chart to correlate the findings from the QC array and those from CMA. “+” means with PCNV/UPD from the QC array or CMA; “-” means without PCNV/UPD findings
Fig. 2
Fig. 2
Most frequent PCNVs in 11,020 ES cases
Fig. 3
Fig. 3
Detection of a gross deletion and a heterozygous pathogenic variant in the WDR19 gene (RefSeq NM_025132) in patient WC5 with a history of end-stage renal disease. a The locations of the deletion and single nucleotide variant in WDR19. The exons 10–13 deletion is indicated by a bar, and the pathogenic variant is indicated by an arrow. b A plot to show the deletion detected by CMA. The deletion is indicated by the red box, and the probes are indicated by bars on the top. c Chromatograph trace to show the heterozygous pathogenic variant detected by ES and confirmed by Sanger sequencing
Fig. 4
Fig. 4
PCNV/UPD detection rate increases with an increase in the number of distinct top-level HPO terms. a A scatterplot showing the trend of PCNV/UPD detection rate as a function of the number of top-level terms. The line represents the fit of a linear model with the shaded area corresponding to the 95% confidence interval. b A bar chart to show the PCNV/UPD detection rate vs number of top-level term for each category of ES divided based on the timing of CMA
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