Evidence map›Paper›PMID 29078313›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2017

Ultraaccurate genome sequencing and haplotyping of single human cells.

Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang

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

Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.

0numbers the graph read from it
0cells of the map it votes in
31citing papers in PubMed
2.0field-weighted citation impact, top 13% 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

31 citing papers in PubMed, 48 citations in OpenAlex.

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  19. Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands.Proceedings of the National Academy of Sciences of the United States of America · 2021
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors at 2 institutions in 1 country.

Wai Keung ChuDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093.
Peter EdgeDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093.
Ho Suk LeeDepartment of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093.
Vikas BansalDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093.
Vineet BafnaDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093; vbafna@cs.ucsd.edu x2huang@ucsd.edu kzhang@eng.ucsd.edu.
Xiaohua HuangDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093; vbafna@cs.ucsd.edu x2huang@ucsd.edu kzhang@eng.ucsd.edu.
Kun ZhangDepartment of Bioengineering, University of California, San Diego, La Jolla, CA 92093; vbafna@cs.ucsd.edu x2huang@ucsd.edu kzhang@eng.ucsd.edu.
University of California, San Diego · USLa Jolla Bioengineering Institute · US

Funding

Single-stranded sequencing using microfluidic reactors (SISSOR)R01HG007836 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HUANG, XIAOHUA, ZHANG, KUN · 2014 to 2017
$3.6M
Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1M
NHGRI NIH HHS R01 HG007836NIGMS NIH HHS R01 GM114362
6 · The paper itself

Abstract

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10

Indexed as

Genome, HumanHaplotypesAllelesCell LineContig MappingFibroblastsHLA AntigensHumansMicrofluidic Analytical TechniquesMutationPolymorphism, Single NucleotideSingle-Cell AnalysisWhole Genome SequencingHLA Antigenshaplotypingmicrofluidicsmutation detectionsingle-cell sequencing

Identifiers

PMID29078313
PMCPMC5703283
OpenAlexW2949696116

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.