Evidence map›Paper›PMID 37106434›Full record

ArticleBMC research notes2023

Construction of high coverage whole-genome sequencing libraries from single colon crypts without DNA extraction or whole-genome amplification.

Zarko Manojlovic, Jordan Wlodarczyk, Cindy Okitsu, Yuxin Jin, David Van Den Berg, Michael R Lieber, Chih-Lin Hsieh

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Whole-genome sequencing ofMicrobiology resource announcements · 2024
    Article
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

7 authors.

Zarko ManojlovicDepartment of Urology, University of Southern California, 1441 Eastlake Ave., NTT5420, Los Angeles, CA, USA.
Jordan WlodarczykDepartment of Surgery, University of Southern California, Los Angeles, CA, USA.
Cindy OkitsuDepartment of Pathology, University of Southern California, Los Angeles, CA, USA.
Yuxin JinDepartment of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
David Van Den BergDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
Michael R LieberDepartment of Pathology, University of Southern California, Los Angeles, CA, USA.
Chih-Lin HsiehDepartment of Urology, University of Southern California, 1441 Eastlake Ave., NTT5420, Los Angeles, CA, USA. hsieh_c@med.usc.edu.

Funding

GENETIC HETEROGENEITY AMONG HUMAN SOMATIC CELLS AND ITS ACCUMULATION WITH AGER01AG067615 · NIA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI HSIEH, CHIH-LIN · 2020 to 2024
$1.4M
NIA NIH HHS R01 AG067615NIH HHS R01 AG 067615
6 · The paper itself

Abstract

objectiveComprehensive and reliable genome-wide variant analysis of a small number of cells has been challenging due to genome coverage bias, PCR over-cycling, and the requirement of expensive technologies. To comprehensively identify genome alterations in single colon crypts that reflect genome heterogeneity of stem cells, we developed a method to construct whole-genome sequencing libraries from single colon crypts without DNA extraction, whole-genome amplification, or increased PCR enrichment cycles.

resultsWe present post-alignment statistics of 81 single-crypts (each contains four- to eight-fold less DNA than the requirement of conventional methods) and 16 bulk-tissue libraries to demonstrate the consistent success in obtaining reliable coverage, both in depth (≥ 30X) and breadth (≥ 92% of the genome covered at ≥ 10X depth), of the human genome. These single-crypt libraries are of comparable quality as libraries generated with the conventional method using high quality and quantities of purified DNA. Conceivably, our method can be applied to small biopsy samples from many tissues and can be combined with single cell targeted sequencing to comprehensively profile cancer genomes and their evolution. The broad potential application of this method offers expanded possibilities in cost-effectively examining genome heterogeneity in small numbers of cells at high resolution.

Indexed as

DNANucleic Acid Amplification TechniquesHigh-Throughput Nucleotide SequencingHumansPolymerase Chain ReactionSequence Analysis, DNAWhole Genome SequencingDNAHigh coverage whole-genome sequencingNext generation sequencingSequencing library construction without DNA extraction

Identifiers

PMID37106434
PMCPMC10142246

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LicenceCC BY
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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.