ArticleGenome medicine2015
Secondary findings and carrier test frequencies in a large multiethnic sample.
Article in Genome medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
33 citing papers in PubMed, 49 citations in OpenAlex.
- The BabySeq project: implementing genomic sequencing in newborns.BMC pediatrics · 2018Trial
- Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals.Journal of human genetics · 2018Trial
- Design of a randomized controlled trial for genomic carrier screening in healthy patients seeking preconception genetic testing.Contemporary clinical trials · 2017Trial
- Article
- A gene pathogenicity tool "GenePy" identifies missed biallelic diagnoses in the 100,000 Genomes Project.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- The impact of the Turkish population variome on the genomic architecture of rare disease traits.Genetics in medicine open · 2024Article
- Article
- Exome and genome sequencing in adults with undiagnosed disease: a prospective cohort study.Journal of medical genetics · 2021Article
- Neurodegenerative Disease Risk in Carriers of Autosomal Recessive Disease.Frontiers in neurology · 2021Review
- Clinical impact of a cancer genomic profiling test using an in-house comprehensive targeted sequencing system.Cancer science · 2020Article
- Article
- Article
- Precision Medicine in Internal Medicine.Annals of internal medicine · 2019Article
- Insights into genetics, human biology and disease gleaned from family based genomic studies.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Review
- Interpretation of Genomic Sequencing Results in Healthy and Ill Newborns: Results from the BabySeq Project.American journal of human genetics · 2019Article
- Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls.Genome medicine · 2018Article
- High-frequency actionable pathogenic exome variants in an average-risk cohort.Cold Spring Harbor molecular case studies · 2018Article
- Genomic sequencing identifies secondary findings in a cohort of parent study participants.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- A systematic analysis of online marketing materials used by providers of expanded carrier screening.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles.American journal of human genetics · 2018Article
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 4 institutions in 2 countries.
Funding
Abstract
backgroundBesides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES.
methodsWe used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups.
resultsIn the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants.
conclusionsBy investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.
Identifiers
What OpenQuestion holds
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.