Evidence map›Paper›PMID 36251442›Full record

ArticleMolecular genetics & genomic medicine2022

Scalable detection of technically challenging variants through modified next-generation sequencing.

Susan Rojahn, Tina Hambuch, Jessika Adrian, Erik Gafni, Alex Gileta, Hannah Hatchell, Britt Johnson, Ben Kallman, Kate Karfilis, Curtis Kautzer and 17 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular genetics & genomic medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

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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

27 authors.

Susan RojahnInvitae, San Francisco, California, USA.ORCID 0000-0001-5888-7693
Tina HambuchInvitae, San Francisco, California, USA.
Jessika AdrianInvitae, San Francisco, California, USA.
Erik GafniInvitae, San Francisco, California, USA.
Alex GiletaInvitae, San Francisco, California, USA.
Hannah HatchellInvitae, San Francisco, California, USA.
Britt JohnsonInvitae, San Francisco, California, USA.
Ben KallmanInvitae, San Francisco, California, USA.
Kate KarfilisInvitae, San Francisco, California, USA.
Curtis KautzerInvitae, San Francisco, California, USA.
Michael KennemerInvitae, San Francisco, California, USA.
Lloyd KirkInvitae, San Francisco, California, USA.
Daniel KvitekInvitae, San Francisco, California, USA.
Jessica LettesInvitae, San Francisco, California, USA.
Fenner MacraeInvitae, San Francisco, California, USA.
Fernando MendezInvitae, San Francisco, California, USA.
Joshua PaulInvitae, San Francisco, California, USA.
Maurizio PellegrinoInvitae, San Francisco, California, USA.
Ronny PreciadoInvitae, San Francisco, California, USA.
Jan RisingerInvitae, San Francisco, California, USA.
Matthew SchultzInvitae, San Francisco, California, USA.
Lindsay SpurkaInvitae, San Francisco, California, USA.
Sajani SwamyInvitae, San Francisco, California, USA.
Rebecca TrutyInvitae, San Francisco, California, USA.
Nathan UsemInvitae, San Francisco, California, USA.
Andrea VelenichInvitae, San Francisco, California, USA.
Swaroop AradhyaInvitae, San Francisco, California, USA.ORCID 0000-0001-6219-2931

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSome clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions).

methodsWe customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes.

resultsOur adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats.

conclusionsNGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.

Indexed as

Fragile X Messenger Ribonucleoprotein 1High-Throughput Nucleotide SequencingGenotypeGlycated HemoglobinHumansMismatch Repair Endonuclease PMS2MutS Homolog 2 ProteinSteroid 21-HydroxylaseCYP21A2 protein, humanFMR1 protein, humanFragile X Messenger Ribonucleoprotein 1Glycated HemoglobinMismatch Repair Endonuclease PMS2MutS Homolog 2 ProteinSteroid 21-Hydroxylasebioinformaticsgenetic testingmolecular geneticsnext-generation sequencing

Identifiers

PMID36251442
PMCPMC9747563

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LicenceCC BY-NC-ND
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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.