Whole Exome Sequencing of Tumor Samples

DNA extracted from frozen biopsies of the primary tumors, metastases and germline were subjected to exome capture using SureSelect Human All Exon v4 (Agilent) and to massively parallel sequencing on an Illumina HiSeq 2000 following validated protocols (19 (link)) (Supplementary Table S2, Supplementary Methods). WES data have been deposited in the Sequence Read Archive (SRP055001).
WES data processing was performed as previously described (19 (link)). Somatic single nucleotide variants (SNVs) were identified using MuTect (v1.0) (20 (link)) and somatic small insertions and deletions (indels) were identified using GATK (v2.7.4) (21 (link)) and the micro-assembly-based Scalpel (v0.1.1) (22 (link)) (Supplementary Methods).

Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link: Access Free Full Text.

Ng C.K., Bidard F.C., Piscuoglio S., Geyer F.C., Lim R.S., de Bruijn I., Shen R., Pareja F., Berman S.H., Wang L., Pierga J.Y., Vincent-Salomon A., Viale A., Norton L., Sigal B., Weigelt B., Cottu P, & Reis-Filho J.S. (2017). Genetic Heterogeneity in Therapy-Naïve Synchronous Primary Breast Cancers and Their Metastases. Clinical cancer research : an official journal of the American Association for Cancer Research, 23(15), 4402-4415.

Publication 2017

SureSelect Human All Exon v4 HiSeq 2000

Biopsies Deletions Exome Exon Frozen Germline Human Indels Insertions Metastases Nucleotide Somatic Tumors

Corresponding Organization : Institut Curie

Other organizations : University Hospital of Basel, Hospital Israelita Albert Einstein, Délégation Paris 5, Université Paris Cité

Top 5 similar protocols

Protocol cited in 5 other protocols

Variable analysis

independent variables

Extraction of DNA from frozen biopsies of the primary tumors, metastases and germline
Exome capture using SureSelect Human All Exon v4 (Agilent)
Massively parallel sequencing on an Illumina HiSeq 2000

dependent variables

Somatic single nucleotide variants (SNVs)
Somatic small insertions and deletions (indels)

control variables

Validated protocols for DNA extraction, exome capture, and massively parallel sequencing (19)

controls

No positive or negative controls are explicitly mentioned in the provided information.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!