Evidence map›Paper›PMID 29642839›Full record

ArticleBMC bioinformatics2018

TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing.

M Heath Farris, Andrew R Scott, Pamela A Texter, Marta Bartlett, Patricia Coleman, David Masters

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

Article in BMC bioinformatics, 2018. 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
0.1field-weighted citation impact, top 53% 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, 2 citations in OpenAlex.

  1. Article
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

6 authors at 3 institutions in 1 country.

M Heath FarrisThe Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA. hfarris@mitre.org.
Andrew R ScottThe Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA.
Pamela A TexterThe Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA.
Marta BartlettThe Homeland Security Systems Engineering and Development Institute (HSSEDI), operated by The MITRE Corporation, McLean, Virginia, USA.
Patricia ColemanThe Department of Homeland Security, U.S. Customs and Border Protection, Washington, DC, USA.
David MastersThe Department of Homeland Security, Science and Technology Directorate, Washington, DC, USA.
Mitre (United States) · USUnited States Customs and Border Protection · USUnited States Department of Homeland Security · US

Funding

Science and Technology Directorate HSHQDC-14-D-00006
6 · The paper itself

Abstract

backgroundSingle nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms.

resultsThe SNP island target identification algorithm (TIA) was developed as a user-tunable system to leverage SNP information within databases. Using data within the 1000 Genomes Project SNP database, human genome regions were identified that contain globally ubiquitous identity-linked SNPs and that were responsive to targeted resequencing on MPS platforms. Algorithmic filters were used to exclude target regions that did not conform to user-tunable SNP island target characteristics. To validate the accuracy of TIA for discovering these identity-linked SNP islands within the human genome, SNP island target regions were amplified from 70 contributor genomic DNA samples using the polymerase chain reaction. Multiplexed amplicons were sequenced using the Illumina MiSeq platform, and the resulting sequences were analyzed for SNP variations. 166 putative identity-linked SNPs were targeted in the identified genomic regions. Of the 309 SNPs that provided discerning power across individual SNP profiles, 74 previously undefined SNPs were identified during evaluation of targets from individual genomes. Overall, DNA samples of 70 individuals were uniquely identified using a subset of the suite of identity-linked SNP islands.

conclusionsTIA offers a tunable genome search tool for the discovery of targeted genomic regions that are scalable in the population frequency and numbers of SNPs contained within the SNP island regions. It also allows the definition of sequence length and sequence variability of the target region as well as the less variable flanking regions for tailoring to MPS platforms. As shown in this study, TIA can be used to discover identity-linked SNP islands within the human genome, useful for differentiating individuals by targeted resequencing on MPS technologies.

Indexed as

AlgorithmsDNAGenome, HumanGenomic IslandsHaplotypesHigh-Throughput Nucleotide SequencingHumansPolymorphism, Single NucleotideReproducibility of ResultsSequence Analysis, DNADNAAlgorithmHuman identityMassively parallel sequencing (MPS)Population frequencySingle nucleotide polymorphism (SNP)

Identifiers

PMID29642839
PMCPMC5896139
OpenAlexW2798947371

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

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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.