Further reading and documentation¶
Please find below some useful links and publications to help you navigate and understand the data.
Research Environment useful links¶
| Link | URL |
|---|---|
| Amazon WorkSpaces (AWS) client download | https://clients.amazonworkspaces.com/ |
| File Transfer Application | https://airlock-staging.extge.co.uk/ |
| Genomics England Service Desk | https://jiraservicedesk.extge.co.uk/servicedesk/customer/portals |
Technical documentation¶
| Document | Version | Used for | Link |
|---|---|---|---|
| Illumina Whole Genome Sequencing Services Guide | December 2015 | 100kGP and GMS | Whole Genome Sequencing Services Guide |
| Illumina Cancer Analysis Services Guide | December 2015 | 100kGP and GMS | Cancer Analysis Services Guide |
| Rare Disease Results Guide | v5.0 | 100kGP | Rare Disease Results Guide |
| Cancer Genome Analysis Guide | v2.28 | 100kGP Dragen realignment and GMS | Cancer Genome Analysis Guide |
| Rare Disease Genome Analysis Guide | v2.2 | GMS | Rare Disease Genome Analysis Guide |
| Cancer Analysis Technical Information Document | v1.11 | 100K NSV4 - check the csv_version column of the cancer_tier_and_domain_variants table to see what version was used for your sample(s) of interest |
Cancer Analysis Technical Information Document |
| PanelApp Handbook | v7 | 100kGP and GMS | PanelApp Handbook |
| International statistical classification of diseases and related health problems (ICD-10) | v10 | 100kGP | ICD10 |
| Exomiser (Improved exome prioritisation of disease genes through cross-species phenotype comparison) | - | 100kGP and GMS | Improved exome prioritisation of disease genes through cross-species phenotype comparison |
| Rare Disease Conditions Phenotypes and Clinical Tests (Clinical Data Models) | v1.9.0 | 100kGP and GMS | Clinical data models |
Previous genome analysis guides
We have listed here the previous versions of the genome analysis guides for rare disease and cancer. Please cross-check the analysis dates of your samples of interest against the document dates to see which versions of the pipelines were applied.
| Document | Version | Date | Notes |
|---|---|---|---|
| Rare disease genome analysis guide | v2.2 | 15/11/2022 | |
| Rare disease genome analysis guide | v2.1 | 16/07/2021 | |
| Rare disease genome analysis guide | v3 | 04/2021 | |
| Cancer genome analysis guide | v2.28 | 30/11/2022 | GMS data and cancer_100K_genomes_realigned_on_pipeline_2 |
| Cancer genome analysis guide | v2.27 | 30/11/2022 | |
| Cancer genome analysis guide | v2.23 | 26/07/2022 | |
| Cancer genome analysis guide | v2.21 | 24/09/2021 | |
| Cancer genome analysis guide | v2.15.2 | 16/07/2021 | |
| Cancer genome analysis guide | v2.15.1 | 04/2021 |
v1.11 of the cancer genome analysis process was used for the 100K genomes project and the VCF files in the cancer_analysis LabKey table.
Publications and other useful links¶
| Publication | URL |
|---|---|
| Improved exome prioritization of disease genes through cross-species phenotype comparison | https://europepmc.org/article/MED/24162188 |
| Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms | https://europepmc.org/article/MED/23736529 |
| Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs | https://europepmc.org/article/MED/22581179 |
| Strelka2: fast and accurate calling of germline and somatic variants | https://europepmc.org/article/MED/30013048 |
| Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications | https://europepmc.org/article/MED/26647377 |
| Canvas: versatile and scalable detection of copy number variants | https://europepmc.org/article/MED/27153601 |
| ExpansionHunter: Detection of long repeat expansions from PCR-free whole-genome sequence data | https://europepmc.org/article/MED/28887402 |
| Platypus: a tool designed for efficient and accurate variant-detection in high-throughput sequencing data | https://europepmc.org/article/MED/25017105 |
| Signatures of Mutational Processes in Human Cancer | https://cancer.sanger.ac.uk/cosmic/signatures |
| PONnoise50SNV: SNVs resulting from systematic mapping and calling artefacts | Filtering artefacts in somatic single nucleotide variant calling using a panel of normals |