ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2014
PATH-SCAN: a reporting tool for identifying clinically actionable variants.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 12 citations in OpenAlex.
- Beyond medically actionable results: an analytical pipeline for decreasing the burden of returning all clinically significant secondary findings.Human genetics · 2021Article
- Article
- Modeling mutant/wild-type interactions to ascertain pathogenicity of PROKR2 missense variants in patients with isolated GnRH deficiency.Human molecular genetics · 2018Article
- Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators.Journal of clinical and translational science · 2017Article
- Big Data Analytics for Genomic Medicine.International journal of molecular sciences · 2017Review
- IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.Journal of the American Medical Informatics Association : JAMIA · 2016Article
- Genetic polymorphisms of pharmacogenomic VIP variants in the Mongol of Northwestern China.BMC genetics · 2016Article
- WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data.Computers in biology and medicine · 2016Article
- Non-Coding Loss-of-Function Variation in Human Genomes.Human heredity · 2016Review
- Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine.Journal of healthcare engineering · 2016Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
The American College of Medical Genetics and Genomics (ACMG) recently released guidelines regarding the reporting of incidental findings in sequencing data. Given the availability of Direct to Consumer (DTC) genetic testing and the falling cost of whole exome and genome sequencing, individuals will increasingly have the opportunity to analyze their own genomic data. We have developed a web-based tool, PATH-SCAN, which annotates individual genomes and exomes for ClinVar designated pathogenic variants found within the genes from the ACMG guidelines. Because mutations in these genes predispose individuals to conditions with actionable outcomes, our tool will allow individuals or researchers to identify potential risk variants in order to consult physicians or genetic counselors for further evaluation. Moreover, our tool allows individuals to anonymously submit their pathogenic burden, so that we can crowd source the collection of quantitative information regarding the frequency of these variants. We tested our tool on 1092 publicly available genomes from the 1000 Genomes project, 163 genomes from the Personal Genome Project, and 15 genomes from a clinical genome sequencing research project. Excluding the most commonly seen variant in 1000 Genomes, about 20% of all genomes analyzed had a ClinVar designated pathogenic variant that required further evaluation.
Indexed as
Identifiers
24297550PMC4008882W2261580330What 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.