Whole Exome Sequencing of sIBM Patients

Indexed genomic DNA libraries were prepared from genomic DNA using TruSeq DNA Preparation Kit (Illumina, San Diego, CA, USA) and exome capture using TruSeq Exome Enrichment Kit (Illumina), according to the manufacturer’s protocol. Sequencing was performed with 100 bp paired-end reads on a HiSeq2000 (Illumina). Reads were aligned to the human reference genome with NovoAlign (Novocraft Technologies, Selangor, Malaysia) or Burrows-Wheeler Aligner.^{18 (link)} Variants were called with SAMtools^{19 (link)} and annotated with SeattleSeq. Coverage across genomic intervals was calculated using BEDTools.^{20 (link)} Genomic coordinates for regions targeted by the whole-exome capture kit were provided by Illumina. Whole exome sequences from 62 sIBM patients were filtered for variants that: 1) had a minor allele frequency of ≤0.001 in the ExAC Database; 2) generated a loss of function variant or a nonsynonymous change; and 3) fulfilled a strict sequence quality as defined by Genesis 2.0 software.

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.

Güttsches A.K., Brady S., Krause K., Maerkens A., Uszkoreit J., Eisenacher M., Schreiner A., Galozzi S., Mertens-Rill J., Tegenthoff M., Holton J.L., Harms M.B., Lloyd T.E., Vorgerd M., Weihl C.C., Marcus K, & Kley R.A. (2017). Proteomics of rimmed vacuoles define new risk allele in inclusion body myositis. Annals of neurology, 81(2), 227-239.

Publication 2016

TruSeq DNA Preparation Kit TruSeq Exome Enrichment Kit HiSeq2000

Bp 100 Exome Genome human Genomic Genomic dna libraries Patients

Corresponding Organization : Hope Center for Neurological Disorders

Other organizations : Southmead Hospital, MRC Prion Unit, University College London, National Hospital for Neurology and Neurosurgery, Columbia University, Johns Hopkins University, Johns Hopkins Medicine

Top 5 similar protocols

Variable analysis

independent variables

TruSeq DNA Preparation Kit (Illumina)
TruSeq Exome Enrichment Kit (Illumina)
HiSeq2000 (Illumina) for sequencing
NovoAlign (Novocraft Technologies) or Burrows-Wheeler Aligner for read alignment
SAMtools for variant calling
SeattleSeq for variant annotation
BEDTools for coverage calculation across genomic intervals

dependent variables

Whole exome sequences from 62 sIBM patients

control variables

Genomic coordinates for regions targeted by the whole-exome capture kit provided by Illumina
Variants filtered for: 1) minor allele frequency ≤0.001 in the ExAC Database, 2) loss of function variant or nonsynonymous change, and 3) strict sequence quality as defined by Genesis 2.0 software

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!