Evidence map›Paper›PMID 24501098›Full record

ArticleBioinformatics (Oxford, England)2014

Visualization and probability-based scoring of structural variants within repetitive sequences.

Eitan Halper-Stromberg, Jared Steranka, Kathleen H Burns, Sarven Sabunciyan, Rafael A Irizarry

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

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.3field-weighted citation impact, top 38% 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

1 citing paper in PubMed, 6 citations in OpenAlex.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 3 institutions in 1 country.

Eitan Halper-StrombergDepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Cente
Jared SterankaDepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USA.
Kathleen H BurnsDepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Cente
Sarven SabunciyanDepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USA.
Rafael A IrizarryDepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USADepartment of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, Computational Bioscience Program, University of Colorado, Denver, Department of Molecular Biology and Genetics, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Department of Pathology, Johns Hopkins University, High Throughput Biology Center, Johns Hopkins University School of Medicine, Johns Hopkins University, Center for Epigenetics, Johns Hopkins University School of Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD and Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, Massachusetts, MA, USA.
Johns Hopkins Hospital · USSidney Kimmel Comprehensive Cancer Center · USHigh Throughput Biology (United States) · US

Funding

Computational Bioscience Program Training GrantT15LM009451 · NLM · UNIVERSITY OF COLORADO DENVER · PI Katherina Kechris-Mays, Arjun Krishnan · 2007 to 2026
$11.7M
Predoctoral Training Program in Human GeneticsT32GM007814 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 1985 to 2021
$10.6M
Overcoming bias and unwanted variability in next generation sequencingR01HG005220 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI IRIZARRY, RAFAEL ANGEL · 2010 to 2018
$3.6M
Transposon Insertion Polymorphisms in Predispositions to Hematopoietic NeoplasiaR01CA163705 · NCI · JOHNS HOPKINS UNIVERSITY · PI BURNS, KATHLEEN H · 2013 to 2017
$1.7M
Mouse Models of Functional Insertion PolymorphismsR01GM103999 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BURNS, KATHLEEN H · 2013 to 2016
$1.2M
NCI NIH HHS R01 CA163705NHGRI NIH HHS R01 HG005220NHGRI NIH HHS R01HG005220NIGMS NIH HHS R01 GM103999NIGMS NIH HHS T32 GM007814NLM NIH HHS T15 LM009451
6 · The paper itself

Abstract

motivationRepetitive sequences account for approximately half of the human genome. Accurately ascertaining sequences in these regions with next generation sequencers is challenging, and requires a different set of analytical techniques than for reads originating from unique sequences. Complicating the matter are repetitive regions subject to programmed rearrangements, as is the case with the antigen-binding domains in the Immunoglobulin (Ig) and T-cell receptor (TCR) loci.

resultsWe developed a probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts. We demonstrate the usefulness of this method in its ability to separate real structural variants from false positives generated with existing upstream analysis tools. We validated our approach using both target-capture and whole-genome experiments. Capture sequencing reads were generated from primary lymphoid tumors, cancer cell lines and an EBV-transformed lymphoblast cell line over the Ig and TCR loci. Whole-genome sequencing reads were from a lymphoblastoid cell-line. AVAILABILITY: We implement our method as an R package available at https://github.com/Eitan177/targetSeqView. Code to reproduce the figures and results are also available.

Indexed as

Genomic Structural VariationCell Line, TransformedCell Line, TumorDNAGenome, HumanGenomicsHigh-Throughput Nucleotide SequencingHumansProbabilityRepetitive Sequences, Nucleic AcidSequence AlignmentSequence Analysis, DNADNA

Identifiers

PMID24501098
PMCPMC4029030
OpenAlexW2130753511

What OpenQuestion 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 OpenQuestion graph.