| Chemicals, Peptides, and Recombinant Proteins |
|
| MLH1 antibody |
Agilent Technologies |
cat. NCL-L-MLH1; RRID: AB_10555424
|
| MSH2 antibody |
Agilent Technologies |
cat. M363901-2; RRID: AB_2631353
|
| MSH6 antibody |
Agilent Technologies |
cat. M364601-2 |
| PMS2 antibody |
BD Biosciences |
cat. 556415; RRID: AB_396410
|
| ATRX antibody |
Sigma-Aldrich |
HPA001906; RRID: AB_1078249
|
| Telomere FISH |
Agilent Technologies |
K532511-8 |
| Schiff’s fuchsin-sulphite reagent |
Sigma-Aldrich |
S5133 |
|
| Deposited data |
|
| WGS data |
This study |
EGA: EGAD00001004162 |
| Methylation array data |
This study |
ArrayExpress: E-MTAB-6961 |
| RNA seq data |
This study |
EGA: EGAD00001004439 |
|
| Software and algorithms |
|
| CaVEMan |
(Varela et al., 2011) |
https://github.com/cancerit/CaVEMan |
| cgpPindel |
(Raine et al., 2015) |
https://github.com/cancerit/cgpPindel |
| BRASS |
(Nik-Zainal et al., 2016) |
https://github.com/cancerit/BRASS |
| ASCAT NGS |
(Van Loo et al., 2010) |
https://github.com/cancerit/ascatNgs |
| Battenberg |
|
https://github.com/cancerit/cgpBattenberg |
| GISTIC 2.0 |
(Mermel et al., 2011) |
http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=216&p=t |
| Telseq |
(Ding et al., 2014) |
https://github.com/zd1/telseq |
| Mutational signatures |
(Alexandrov et al., 2018) |
https://uk.mathworks.com/matlabcentral/fileexchange/38724-sigprofiler |
| dndSCV |
(Martincorena et al., 2017) |
https://github.com/im3sanger/dndscv |
| CIVIC database |
(Griffith et al., 2017) |
https://civicdb.org/home |
| Genie database |
(AACR Project GENIE Consortium, 2017) |
http://www.aacr.org/Research/Research/Pages/aacr-project-genie.aspx#.WyD4IjMzq34 |
| MSKCC hotspots database |
(Chang et al., 2016) |
http://cancerhotspots.org/ |
| Encode blacklist |
(Encode Project Consortium, 2012) |
https://www.encodeproject.org/annotations/ENCSR636HFF/ |
| ExAC database |
(Lek et al., 2016) |
http://exac.broadinstitute.org/ |
| Variant Effect Predictor |
(McLaren et al., 2016) |
https://www.ensembl.org/info/docs/tools/vep/index.html |
| Recurrent rearrangements |
This paper |
https://github.com/UCL-Research-Department-of-Pathology/RETREAD |
| Chromothripsis identification |
This paper |
https://github.com/UCL-Research-Department-of-Pathology/CODER |
| Copy number signatures |
This paper |
https://github.com/UCL-Research-Department-of-Pathology/CONUSIG |
| Mutation triaging |
This paper |
https://github.com/UCL-Research-Department-of-Pathology/Triagen |
| Rearrangment signatures |
(Nik-Zainal et al., 2016), this paper |
https://github.com/UCL-Research-Department-of-Pathology/RESIN |
| Timing whole genome doubling |
(Dentro et al., 2017) |
https://github.com/galder-max/USARCtiming |
| HISAT2 |
(Kim et al., 2015) |
https://github.com/infphilo/hisat2 |
| Stringtie |
(Pertea et al., 2015) |
https://github.com/gpertea/stringtie |
| Mutect2 |
(Van der Auwera et al., 2013) |
https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef |
| Lumpy |
(Layer et al., 2014) |
https://github.com/arq5x/lumpy-sv |
| ASCAT |
(Van Loo et al., 2010) |
https://github.com/Crick-CancerGenomics/ascat |
