Evidence map›Paper›PMID 26265630›Full record

ArticleCirculation research2015

A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases.

Kitchener D Wilson, Peidong Shen, Eula Fung, Ioannis Karakikes, Angela Zhang, Kolsoum InanlooRahatloo, Justin Odegaard, Karim Sallam, Ronald W Davis, George K Lui and 3 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Circulation research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed, 1 pooled it
3.6field-weighted citation impact, top 6% of its field
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

28 citing papers in PubMed, 1 synthesis or guideline pooled it, 41 citations in OpenAlex.

  1. Genetic evaluation of cardiomyopathy: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG).Genetics in medicine : official journal of the American College of Medical Genetics · 2018
    Guideline
  2. Review
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  4. Article
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  7. The Genetic Evaluation of Dilated Cardiomyopathy.Structural heart : the journal of the Heart Team · 2023
    Review
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  9. Article
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  11. Article
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors at 1 institution in 1 country.

Kitchener D WilsonFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA. kitchwilson@stanford.edu joewu@stanford.edu.
Peidong ShenFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Eula FungFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Ioannis KarakikesFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Angela ZhangFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Kolsoum InanlooRahatlooFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Justin OdegaardFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Karim SallamFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Ronald W DavisFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
George K LuiFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Euan A AshleyFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Curt ScharfeFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA.
Joseph C WuFrom the Department of Pathology (K.D.W., E.F., J.O., C.S.), and Department of Biochemistry (P.S., R.W.D.), Stanford Cardiovascular Institute (K.D.W., I.K., A.Z., K.I., J.O., K.S., G.K.L., E.A.A., J.C.W.), Stanford Genome Technology Center (P.S., E.F., R.W.D., C.S.), Department of Medicine, Division of Cardiology (K.S., G.K.L., E.A.A., J.C.W.), Stanford Adult Congenital Heart Disease Clinic (J.C.W., G.K.L.), and Department of Radiology (J.C.W.), Stanford University, CA. kitchwilson@stanford.edu joewu@stanford.edu.
Norwegian Womens Public Health Association · NO

Funding

WHOLE YEAST GENOME TRANSCRIPTIONAL AND FUNCTIONAL GENE MAPS--A FEASIBILITY STUDYP01HG000205 · NHGRI · STANFORD UNIVERSITY · PI DAVIS, RONALD WAYNE, HOWE, ROGER THOMAS · 1990 to 2016
$120.9M
Biorepository of Human iPSCs for Studying Dilated and Hypertrophic CardiomyopathyR24HL117756 · NHLBI · STANFORD UNIVERSITY · PI BUSTAMANTE, CARLOS DANIEL, SNYDER, MICHAEL P. · 2014 to 2018
$8.8M
Human Induced Pluripotent Stem Cells for Cardiovascular Disease ModelingR01HL113006 · NHLBI · STANFORD UNIVERSITY · PI WU, JOSEPH C. · 2012 to 2025
$6.8M
Genome Editing of Human iPSCs to Study Inherited Hypertrophic CardiomyopathyR01HL126527 · NHLBI · STANFORD UNIVERSITY · PI QI, LEI STANLEY, WU, JOSEPH C. · 2015 to 2022
$5.4M
Training in Myocardial Biology at Stanford (TIMBS)T32HL094274 · NHLBI · STANFORD UNIVERSITY · PI Euan A Ashley, Daniel Bernstein · 2010 to 2026
$5.0M
Technology development for rapid detection and diagnosis of metabolic disordersR01HD081355 · NICHD · YALE UNIVERSITY · PI SCHARFE, CURT · 2014 to 2016
$866k
NHGRI NIH HHS P01 HG000205NHLBI NIH HHS R01 HL113006NHLBI NIH HHS R01 HL126527NHLBI NIH HHS R24 HL117756NHLBI NIH HHS T32 HL094274NICHD NIH HHS R01 HD081355
6 · The paper itself

Abstract

rationaleThousands of mutations across >50 genes have been implicated in inherited cardiomyopathies. However, options for sequencing this rapidly evolving gene set are limited because many sequencing services and off-the-shelf kits suffer from slow turnaround, inefficient capture of genomic DNA, and high cost. Furthermore, customization of these assays to cover emerging targets that suit individual needs is often expensive and time consuming.

objectiveWe sought to develop a custom high throughput, clinical-grade next-generation sequencing assay for detecting cardiac disease gene mutations with improved accuracy, flexibility, turnaround, and cost. METHODS AND

resultsWe used double-stranded probes (complementary long padlock probes), an inexpensive and customizable capture technology, to efficiently capture and amplify the entire coding region and flanking intronic and regulatory sequences of 88 genes and 40 microRNAs associated with inherited cardiomyopathies, congenital heart disease, and cardiac development. Multiplexing 11 samples per sequencing run resulted in a mean base pair coverage of 420, of which 97% had >20× coverage and >99% were concordant with known heterozygous single nucleotide polymorphisms. The assay correctly detected germline variants in 24 individuals and revealed several polymorphic regions in miR-499. Total run time was 3 days at an approximate cost of $100 per sample.

conclusionsAccurate, high-throughput detection of mutations across numerous cardiac genes is achievable with complementary long padlock probe technology. Moreover, this format allows facile insertion of additional probes as more cardiomyopathy and congenital heart disease genes are discovered, giving researchers a powerful new tool for DNA mutation detection and discovery.

Indexed as

Cost-Benefit AnalysisBase SequenceGene TargetingHeart DiseasesHigh-Throughput Nucleotide SequencingHumansMolecular Sequence DataPolymorphism, Single NucleotideTime Factorscardiomyopathiescardiovascular diseasescongenital heart diseasegenetic testingmicroRNAsnext generation sequencing

Identifiers

PMID26265630
PMCPMC4568077
OpenAlexW2153910436

What OpenQuestion holds

Textmetadata
LicenceTDM
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 OpenQuestion graph.