Evidence map›Paper›PMID 25447460›Full record

ArticleAnalytical biochemistry2015

Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots.

T Nguyen-Dumont, M Mahmoodi, F Hammet, T Tran, H Tsimiklis, Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), G G Giles, J L Hopper, Australian Breast Cancer Family Registry, M C Southey and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Analytical biochemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. 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

11 authors.

T Nguyen-DumontGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
M MahmoodiGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
F HammetGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
T TranGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
H TsimiklisGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab)
G G GilesCancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia.
J L HopperCentre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Parkville, Victoria 3010, Australia.
Australian Breast Cancer Family Registry
M C SoutheyGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
D J ParkGenetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia. Electronic address: djp@unimelb.edu.au.

Funding

Breast Cancer Family Registry CohortUM1CA164920 · NCI · CANCER PREVENTION INSTIT OF CALIFORNIA · PI ANDRULIS, IRENE, BUYS, SAUNDRA S · 2012 to 2017
$12.7M
A comprehensive approach to breast cancer susceptibility across the risk spectrumR01CA155767 · NCI · UNIVERSITY OF UTAH · PI GOLDGAR, DAVID E., SOUTHEY, MELISSA · 2011 to 2015
$2.2M
NCI NIH HHS R01 CA155767NCI NIH HHS R01CA155767NCI NIH HHS UM1 CA164920NCI NIH HHS UM1CA164920
6 · The paper itself

Abstract

Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.

Indexed as

Dried Blood Spot TestingBreast NeoplasmsCell LineDNADNA Mutational AnalysisFemaleGenetic Predisposition to DiseaseGenetic TestingHumansDNAArchival DNADried blood spotGuthrie CardHi-PlexMassively parallel sequencingTargeted sequencing

Identifiers

PMID25447460
PMCPMC4275364

What OpenQuestion holds

Textmetadata
LicenceTDM
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.