Whole exome sequencing (exome-seq) of mouse tumors was carried out using
tissue frozen in RNA later (Ambion) at -80 °C. DNA was isolated using
the DNeasy Blood & Tissue Kit (Qiagen). Exome capture was carried out
with 2ug of DNA using the Agilent SureSelectXT kit. Sequencing to generate
paired-end100bp reads were obtained using isolated whole exomes sequenced on the
Illumina HiSeq 2500 platform. Our exome-seq pipeline produced a mean coverage of
195X within coding regions. Sequencing reads were aligned to the mouse reference
genome sequence (mm9) using BWA. SAM to BAM conversion was carried out using
Picard tools, and local realignment around indels with base quality score
recalibration was performed using the Genome Analysis Toolkit (GATK). Single
nucleotide variants (SNVs) were called using (GATK). The annotation of
non-synonymous SNVs was performed using Annovar. Comparison to human BCC
mutational landscape was performed using previously published variants
47 (link).
Smo mutation was identified by calling variants on
unfiltered alignment files using Samtools and annotated using snpEff using the
GRCm38.71 genome.
tissue frozen in RNA later (Ambion) at -80 °C. DNA was isolated using
the DNeasy Blood & Tissue Kit (Qiagen). Exome capture was carried out
with 2ug of DNA using the Agilent SureSelectXT kit. Sequencing to generate
paired-end100bp reads were obtained using isolated whole exomes sequenced on the
Illumina HiSeq 2500 platform. Our exome-seq pipeline produced a mean coverage of
195X within coding regions. Sequencing reads were aligned to the mouse reference
genome sequence (mm9) using BWA. SAM to BAM conversion was carried out using
Picard tools, and local realignment around indels with base quality score
recalibration was performed using the Genome Analysis Toolkit (GATK). Single
nucleotide variants (SNVs) were called using (GATK). The annotation of
non-synonymous SNVs was performed using Annovar. Comparison to human BCC
mutational landscape was performed using previously published variants
47 (link).
Smo mutation was identified by calling variants on
unfiltered alignment files using Samtools and annotated using snpEff using the
GRCm38.71 genome.
