Evidence map›Paper›PMID 12709267›Full record

ArticleBMC bioinformatics2003

SNP haplotype tagging from DNA pools of two individuals.

Josephine Hoh, Fumihiko Matsuda, Xu Peng, Daniela Markovic, Mark G Lathrop, Jurg Ott

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. MPDA: microarray pooled DNA analyzer.BMC bioinformatics · 2008
    Article
  2. Article
  3. 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

6 authors.

Josephine HohLaboratory of Statistical Genetics, Rockefeller University, New York, NY 10021, USA. jhoh@linkage.rockefeller.edu
Fumihiko Matsuda
Xu Peng
Daniela Markovic
Mark G Lathrop
Jurg Ott

Funding

LINKAGE ANALYSIS METHODS FOR HUMAN GENE MAPPINGR01HG000008 · NHGRI · ROCKEFELLER UNIVERSITY · PI OTT, JURG · 1990 to 2004
$1.2M
Statistical Methods to Interpret Genomic DataK25HG000060 · NHGRI · YALE UNIVERSITY · PI HOH, JOSEPHINE · 2002 to 2006
$579k
QUANTITATIVE METHODS TO MAP GENES FOR COMPLEX TRAITSR01MH059492 · NIMH · ROCKEFELLER UNIVERSITY · PI OTT, JURG · 2000 to 2002
$415k
NHGRI NIH HHS K25 HG000060NHGRI NIH HHS K25-HG00060NHGRI NIH HHS R01 HG000008NHGRI NIH HHS R01-HG00008NIMH NIH HHS R01-MH59492
6 · The paper itself

Abstract

backgroundDNA pooling is a technique to reduce genotyping effort while incurring only minor losses in accuracy of allele frequency estimates for single nucleotide polymorphism (SNP) markers.

resultsWe present an algorithm for reconstructing haplotypes (alleles for multiple SNPs on same chromosome) from pools of two individual DNAs, in which Hardy-Weinberg equilibrium conditions or other assumptions are not required. The program outputs, in addition to inferred haplotypes, a minimal number of haplotype-tagging SNPs that are identified after an exhaustive search procedure.

conclusionOur method and algorithms lead to a significant reduction in genotyping effort, for example, in case-control disease association studies while maintaining the possibility of reconstructing haplotypes under very general conditions.

Indexed as

AdducinsAlgorithmsAllelesCalmodulin-Binding ProteinsComputational BiologyCytoskeletal ProteinsDNAGenotypeHaplotypesHumansPhenotypePolymorphism, Single NucleotideAdducinsCalmodulin-Binding ProteinsCytoskeletal ProteinsDNA

Identifiers

PMID12709267
PMCPMC156884

What OpenQuestion holds

Textmetadata
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.