Trial reportProceedings of the National Academy of Sciences of the United States of America2016
Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage.
Trial report in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed, 71 citations in OpenAlex.
- Humans homozygous for rare or common hypomorphic IL23R variants are prone to tuberculosis.The Journal of experimental medicine · 2026Article
- A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure.Genome medicine · 2025Article
- Human LY9 governs CD4Science immunology · 2025Article
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- ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis.medRxiv : the preprint server for health sciences · 2024Article
- FLT3L governs the development of partially overlapping hematopoietic lineages in humans and mice.Cell · 2024Article
- Helper T cell immunity in humans with inherited CD4 deficiency.The Journal of experimental medicine · 2024Article
- Article
- Exome sequencing of UK birth cohorts.Wellcome open research · 2024Article
- Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients.Nature communications · 2023Article
- Human IL-23 is essential for IFN-γ-dependent immunity to mycobacteria.Science immunology · 2023Article
- Article
- Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis.The Journal of experimental medicine · 2023Article
- Impaired IL-23-dependent induction of IFN-γ underlies mycobacterial disease in patients with inherited TYK2 deficiency.The Journal of experimental medicine · 2022Article
- Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia.The Journal of experimental medicine · 2022Article
- Homozygous Pro1066ArgLife (Basel, Switzerland) · 2022Article
- A novel mutation in SLC39A7 identified in a patient with autosomal recessive agammaglobulinemia: The impact of the J Project.Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology · 2022Article
- Inherited PD-1 deficiency underlies tuberculosis and autoimmunity in a child.Nature medicine · 2021Article
- Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to multiple infectious agents.The Journal of clinical investigation · 2021Article
- X-linked recessive TLR7 deficiency in ~1% of men under 60 years old with life-threatening COVID-19.Science immunology · 2021Observational
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 20 institutions in 14 countries.
Funding
Abstract
Principal component analysis (PCA), homozygosity rate estimations, and linkage studies in humans are classically conducted through genome-wide single-nucleotide variant arrays (GWSA). We compared whole-exome sequencing (WES) and GWSA for this purpose. We analyzed 110 subjects originating from different regions of the world, including North Africa and the Middle East, which are poorly covered by public databases and have high consanguinity rates. We tested and applied a number of quality control (QC) filters. Compared with GWSA, we found that WES provided an accurate prediction of population substructure using variants with a minor allele frequency > 2% (correlation = 0.89 with the PCA coordinates obtained by GWSA). WES also yielded highly reliable estimates of homozygosity rates using runs of homozygosity with a 1,000-kb window (correlation = 0.94 with the estimates provided by GWSA). Finally, homozygosity mapping analyses in 15 families including a single offspring with high homozygosity rates showed that WES provided 51% less genome-wide linkage information than GWSA overall but 97% more information for the coding regions. At the genome-wide scale, 76.3% of linked regions were found by both GWSA and WES, 17.7% were found by GWSA only, and 6.0% were found by WES only. For coding regions, the corresponding percentages were 83.5%, 7.4%, and 9.1%, respectively. With appropriate QC filters, WES can be used for PCA and adjustment for population substructure, estimating homozygosity rates in individuals, and powerful linkage analyses, particularly in coding regions.
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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.