Evidence map›Paper›PMID 25505899›Full record

ArticleFrontiers in immunology2014

Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis.

Guang Lan Zhang, Derin B Keskin, Hsin-Nan Lin, Hong Huang Lin, David S DeLuca, Scott Leppanen, Edgar L Milford, Ellis L Reinherz, Vladimir Brusic

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

Article in Frontiers in immunology, 2014. 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
0.1field-weighted citation impact, top 47% 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

0 citing papers in PubMed, 3 citations in OpenAlex.

No citing paper in PubMed yet.

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

9 authors at 4 institutions in 2 countries.

Guang Lan ZhangCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA.
Derin B KeskinCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA.
Hsin-Nan LinCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Institute of Information Science, Academia Sinica , Taipei , Taiwan.
Hong Huang LinCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Boston University School of Medicine , Boston, MA , USA.
David S DeLucaCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA.
Scott LeppanenAgilent Technologies, Inc. , Santa Clara, CA , USA.
Edgar L MilfordDepartment of Medicine, Harvard Medical School , Boston, MA , USA ; Histocompatibility and Tissue Typing Laboratory, Brigham and Women's Hospital , Boston, MA , USA.
Ellis L ReinherzCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute , Boston, MA , USA.
Vladimir BrusicCancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Computer Science, Metropolitan College, Boston University , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA.
Harvard University · USAgilent Technologies (United States) · USInstitute of Information Science, Academia Sinica · TWMetropolitan College of New York · US

Funding

Bioinformatics Approach to Influenza A/H1N1 Vaccine Immune ProfilingU01AI089859 · NIAID · MAYO CLINIC ROCHESTER · PI POLAND, GREGORY A. · 2010 to 2015
$33.8M
Crossprotective CTL Against InfluenzaU01AI090043 · NIAID · DANA-FARBER CANCER INST · PI REINHERZ, ELLIS L · 2010 to 2015
$6.4M
NIAID NIH HHS U01 AI089859NIAID NIH HHS U01 AI090043
6 · The paper itself

Abstract

Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world's populations, benefiting both global public health and personalized health care.

Indexed as

HLA disease associationHLA typingpopulation typing

Identifiers

PMID25505899
PMCPMC4245923
OpenAlexW2096645456

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.