ArticleGenetics in medicine : official journal of the American College of Medical Genetics2018
Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Overview of next-generation sequencing to the molecular diagnosis of inborn errors of immunity in Brazil: a systematic review.Frontiers in immunology · 2026Pooled it
- Exome sequencing early in outpatient evaluation in NCGENES 2: Changing the course of the diagnostic odyssey?HGG advances · 2026Article
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- Combined genomics and proteomics unveils elusive variants and vast aetiologic heterogeneity in dystonia.Brain : a journal of neurology · 2025Article
- Comparison of next‑generation sequencing quality metrics and concordance in the detection of cancer‑specific molecular alterations between formalin‑fixed paraffin‑embedded and fresh‑frozen samples in comprehensive genomic profiling with the Illumina® TruSight Oncology 500 assay.Experimental and therapeutic medicine · 2025Article
- Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.Genome research · 2024Article
- Paired comparison of the analytical performance between the Oncomine™ Comprehensive Assay v3 and whole-exome sequencing of ovarian cancer tissue.Molecular biology reports · 2024Article
- Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.medRxiv : the preprint server for health sciences · 2024Article
- Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities-A Narrative Review.Children (Basel, Switzerland) · 2023Review
- A robust pipeline for ranking carrier frequencies of autosomal recessive and X-linked Mendelian disorders.NPJ genomic medicine · 2022Article
- Article
- High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population.American journal of human genetics · 2021Article
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- Considerations for whole exome sequencing unique to prenatal care.Human genetics · 2020Review
- Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families.BMC medical genomics · 2020Article
- A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data.Genome medicine · 2020Article
- Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution.Frontiers in pediatrics · 2020Review
- Exome sequencing in genetic disease: recent advances and considerations.F1000Research · 2020Review
- Methodological differences can affect sequencing depth with a possible impact on the accuracy of genetic diagnosis.Genetics and molecular biology · 2020Article
Corrections and comments
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Authors and funding
32 authors.
Funding
Abstract
purposeAs massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications.
methodsTo enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest. We used this framework to examine sequencing data from 500 patients generated in 10 projects at sequencing centers in the National Human Genome Research Institute/National Cancer Institute Clinical Sequencing Exploratory Research Consortium.
resultsThis approach identified reduced coverage regions in clinically relevant genes, including known clinically relevant loci that were uniquely missed at individual centers, in multiple centers, and in all centers.
conclusionThis report provides a process road map for clinical sequencing centers looking to perform similar analyses on their data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.