HLA Typing and Mutation Calling from Normal and Tumor Whole Genome Sequencing Data with ALPHLARD-NT.

Shuto Hayashi, Seiya Imoto

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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

–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

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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.

No citing paper in PubMed yet.

4 · The record

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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

2 authors.

Shuto HayashiDepartment of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan. s-haya.csb@tmd.ac.jp.

Seiya ImotoHuman Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

HLA somatic mutations can alter the expression and function of HLA molecules, which in turn affect the ability of the immune system to recognize and respond to cancer cells. Therefore, it is crucial to accurately identify HLA somatic mutations to enhance our understanding of the interaction between cancer and the immune system and improve cancer treatment strategies. ALPHLARD-NT is a reliable tool that can accurately identify HLA somatic mutations as well as HLA genotypes from whole genome sequencing data of paired normal and tumor samples. Here, we provide a comprehensive guide on how to use ALPHLARD-NT and interpret the results.

Indexed as

Histocompatibility TestingHLA AntigensMutationNeoplasmsWhole Genome SequencingAllelesComputational BiologyGenome, HumanGenotypeHigh-Throughput Nucleotide SequencingHumansSoftwareHLA AntigensBayesian statistical modelBioinformaticsHLA mutation callingHLA typingIn silicoWhole genome sequencing

Identifiers

PMID38907893

DOI10.1093/bioinformatics/btp352

What OpenQuestion holds

Textmetadata

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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.