Evidence map›Paper›PMID 37790445›Full record

ArticleResearch square2023

Genetic Sex Validation for Sample Tracking in Clinical Testing.

Jianhong Hu, Viktoriya Korchina, Hana Zouk, Maegan V Harden, David Murdock, Alyssa Macbeth, Steven M Harrison, Niall Lennon, Christie Kovar, Adithya Balasubramanian and 19 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

29 authors at 8 institutions in 1 country.

Jianhong HuBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Viktoriya KorchinaBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Hana ZoukLaboratory for Molecular Medicine (LMM), Mass General Brigham.
Maegan V HardenBroad Institute of MIT and Harvard.
David MurdockBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Alyssa MacbethBroad Institute of MIT and Harvard.
Steven M HarrisonLaboratory for Molecular Medicine (LMM), Mass General Brigham.
Niall LennonBroad Institute of MIT and Harvard.
Christie KovarBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Adithya BalasubramanianBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Lan ZhangBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Gauthami ChandanavelliBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Divya PashamBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Robb RowleyNational Human Genome Research Institute.
Ken WileyNational Human Genome Research Institute.
Maureen E SmithNorthwestern University Feinberg School of Medicine.
Adam GordonNorthwestern University Feinberg School of Medicine.
Gail P JarvikUniversity of Washington Medical Center.
Patrick SleimanChildren's Hospital of Philadelphia.
Melissa A KellyGenomic Medicine Institute, Geisinger.
Harris T BlandVanderbilt University Medical Center.
Mullai MuruganBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Eric VennerBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Eric BoerwinkleBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Cynthia ProwsCincinnati Children's Hospital Medical Center.
Lisa MahantaLaboratory for Molecular Medicine (LMM), Mass General Brigham.
Heidi L RehmBroad Institute of MIT and Harvard.
Richard A GibbsBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Donna M MuznyBaylor College of Medicine, Human Genome Sequencing Center (HGSC).
Baylor College of Medicine · USBroad Institute · USMass General Brigham · USNational Human Genome Research Institute · USChildren's Hospital of Philadelphia · USCincinnati Children's Hospital Medical Center · USUniversity of Washington Medical Center · USVanderbilt University Medical Center · US

Funding

Technologies and Resources CoreU54MD007593 · NIMHD · MEHARRY MEDICAL COLLEGE · PI ADUNYAH, SAMUEL EVANS · 2012 to 2018
$24.7M
Genomic Basis of Susceptibility to COVID-19 Infection and its ComplicationsU01HG006379 · NHGRI · MAYO CLINIC ROCHESTER · PI Richard R. Sharp · 2011 to 2026
$16.5M
Finding Genomic Profiles of COVID-19 Phenotypes from the EHRU01HG008685 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ELIZABETH W KARLSON, Matthew S Lebo · 2015 to 2026
$13.6M
Variation, Function, and Disease Supplement ProgramU01HG008657 · NHGRI · UNIVERSITY OF WASHINGTON · PI David Russell Crosslin, Gail Pairitz Jarvik · 2015 to 2026
$13.4M
OMOP information model for eMERGE phenotypingU01HG008680 · NHGRI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Wendy K Chung, GEORGE M HRIPCSAK · 2015 to 2026
$13.3M
DNA Sequencing Support for the eMERGE NetworkU01HG008664 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2015 to 2019
$10.9M
Global Alliance for Genomic Health (GA4GH)U01HG008676 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI LENNON, NIALL JOHN, REHM, HEIDI L · 2015 to 2019
$8.6M
The Electronic Medical Records and Genomics (eMERGE) Network Phase III Coordinating Center (U01)U01HG008701 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI PETERSON, JOSEPH F. · 2015 to 2019
$7.1M
VGER, the Vanderbilt Genome-Electronic Records ProjectU01HG008672 · NHGRI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI DENNY, JOSHUA C., RODEN, DAN M · 2015 to 2019
$5.1M
The Future of Genomics Medicine in Patient Care: Contributions from CHOPU01HG008684 · NHGRI · CHILDREN'S HOSP OF PHILADELPHIA · PI HAKONARSON, HAKON · 2015 to 2019
$5.0M
OMOP information model for eMERGE phenotypingU01HG008679 · NHGRI · GEISINGER CLINIC · PI WILLIAMS, MARC S. · 2015 to 2019
$4.4M
Better Outcomes for Children: Promoting Excellence in Healthcare Genomics to Inform PolicyU01HG008666 · NHGRI · CINCINNATI CHILDRENS HOSP MED CTR · PI HARLEY, JOHN BARKER · 2015 to 2019
$4.2M
NHGRI NIH HHS U01 HG006379NHGRI NIH HHS U01 HG008657NHGRI NIH HHS U01 HG008664NHGRI NIH HHS U01 HG008666NHGRI NIH HHS U01 HG008672NHGRI NIH HHS U01 HG008673NHGRI NIH HHS U01 HG008676NHGRI NIH HHS U01 HG008679NHGRI NIH HHS U01 HG008680NHGRI NIH HHS U01 HG008684NHGRI NIH HHS U01 HG008685NHGRI NIH HHS U01 HG008701NIMHD NIH HHS U54 MD007593
6 · The paper itself

Abstract

Objective: Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. Results: Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.

Indexed as

Clinical testingNext Generation Sequencing (NGS)Sex concordanceSNP genotyping

Identifiers

PMID37790445
PMCPMC10543510
OpenAlexW4386599912

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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 Socratic graph.