Metadata record for the manuscript: Rare Deleterious Germline Variants and Risk of Lung Cancer
Creators: name: Liu, Yanhong
name: Xia, Jun
name: McKay, James
name: Tsavachidis, Spiridon
name: Xiao, Xiangjun
name: Spitz, Margaret R.
name: Cheng, Chao
name: Byun, Jinyoung
name: Hong, Wei
name: Li, Yafang
name: Zhu, Dakai
name: Song, Zhuoyi
name: Rosenberg, Susan M
name: Scheurer, Michael E.
name: Kheradmand, Farrah
name: Pikielny, Claudio W.
name: Lusk, Christine M.
name: Schwartz, Ann G.
name: Wistuba, Ignacio I.
name: Cho, Michael H.
name: Silverman, Edwin K.
name: Bailey-Wilson, Joan
name: Pinney, Susan M.
name: Anderson, Marshall
name: Kupert, Elena
name: Gaba, Colette
name: Mandal, Diptasri
name: You, Ming
name: Andrade, Mariza de
name: Yang, Ping
name: Liloglou, Triantafillos
name: Davies, Michael P.A.
name: Lissowska, Jolanta
name: Swiatkowska, Beata
name: Zaridze, David
name: Mukeriya, Anush
name: Janout, Vladimir
name: Holcatova, Ivana
name: Mates, Dana
name: Stojsic, Jelena
name: Scelo, Ghislaine
name: Brennan, Paul
name: Liu, Geoffrey
name: Field, John K.
name: Hung, Rayjean J.
name: Christiani, David C.
name: Amos, Christopher I.
Publisher: name: figshare
Year: 2021
Subjects: Medical and Health Sciences not elsewhere classified
Diseases
Cancer
Biological Sciences not elsewhere classified
Epidemiology

description: <b>Summary</b>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “Rare Deleterious Germline Variants
and Risk of Lung Cancer”.

The
related study reports whole exome plus targeted sequencing of germline DNA on
1,045 lung cancer (LC) cases and 885 controls in the discovery set. To unveil
the inherited causal variants, the focus was on rare and predicted deleterious
variants and small indels enriched in cases or controls. Promising candidates
were further validated in a series of 26,803 LCs and 555,107 controls.

 

<b>Data
access</b>

The
data that support the findings of this study are available via the <i>dbGaP</i> (database of genotypes and
phenotypes) repository. The data are controlled-access, so interested parties
will need to request access—information on how to do so can be found on pages
linked to below. The access numbers are https://identifiers.org/dbgap:phs000878.v2.p1
for Transdisciplinary Research in Cancer of the Lung (TRICL) study, https://identifiers.org/dbgap:phs001273.v1.p1
for the OncoArray study, https://identifiers.org/dbgap:phs001681.v1.p1
for the Affymetrix study, https://identifiers.org/dbgap:phs000629.v1.p1
for part of the Genetic Epidemiology of Lung Cancer Consortium (GELCC) study, and
https://identifiers.org/dbgap:phs000178.v9.p8
for The Cancer Genome Atlas (TCGA) study.<br>

2
files are not publicly available in order to protect patient privacy. These
are: ‘TRICL WES.xlsx’ (underlying Supplementary Table 2 and Supplementary
Figure 3) and ‘TRICL WES.bam’ (underlying Supplementary Figure 2). These data
are only available to authorized researchers who have submitted an IRB
application. Please email the corresponding author for access.

Data
underlying Supplementary Table 5 and Supplementary Figure 5 are a publicly available
resource available from the STRING (Search Tool for the Retrieval of
Interacting Genes) website: http://string-db.org/.
The file used in this study was ‘Protein-Protein Interaction Networks
Functional Enrichment Analysis-STRING.txt’. 

Sources
of other datasets used in this study are: the UKB dataset can be downloaded
from the UK Biobank at www.ukbiobank.ac.uk.
The GnomAD dataset can be downloaded from the Genome Aggregation Database at https://gnomad.broadinstitute.org/.
 

 

The
corresponding author is: Christopher I. Amos, Institute for Clinical and
Translational Research, Baylor College of Medicine, Houston, TX 77030, Email:
Chris.Amos@bcm.edu, Phone: (713) 798-2102.

<br>
<b>Name of Institutional Review Board or ethics
committee that approved the study <br>
</b>The study was approved by the
institutional review board of all sites accruing participants.