Additional file 2: Figure S1. of Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing

Numbers of Candidate SV Calls Before Filtering Process. The numbers of candidate SV calls detected in 10 samples of different genetic backgrounds before any filtering process. The numbers of total SVs include ITX (intra-chromosomal translocations), DELs (deletions), INV (inversions), INS (insertions), and CTXs (inter-chromosomal translocations) in 10 sequenced samples, including 6 tumor samples (119J, 125J, 196J, 202J, 46J, and 90J) and 4 control samples (control 1, control 2, kidney and wt B6) plus 129S1 whose sequences were downloaded from Sanger’s Institute (see details in Methods). (PDF 361 kb

Additional file 1: Table S1 of Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing

The numbers of CTXs in each sample after filtering process and chromosome coordinates of all CTXs. 10 sequenced samples include 6 tumor samples (119J, 125J, 196J, 202J, 46J, and 90J) and 4 control samples (mouse control 1, mouse control 2, kidney and wt B6) plus 129S1 whose sequences were downloaded from Sanger’s Institute (see details in Methods). (XLSX 541 kb

Bioinformatics filtering algorithm.

<p>Shown are bioinformatics analysis tools used and individual and mean variant numbers at each step of filtering with resulting decrease in variant numbers at each decision step.</p

Visualization of NGS alignment and chromatogram from Sanger sequencing confirming the <i>TNNT2 Arg173Trp</i> variant.

<p>The alignment and Sanger sequencing profiles of the TNNT2 R173W variant are shown. A) C>T variant alignment reads of Arg173Trp variant B) (inset) Chromatogram of C>T variant of Arg173Trp variant from Sanger sequencing; arrow depicts the c.517T C>T (chr1∶201,332,477) position.</p

Clinical features of key member of family AD-FDC1 and AD-FDC27.

<p>NYHA - New York Heart Association class; ECG - Electrocardiogram; LVEDD - left ventricular end-diastolic diameter; LVEF - left ventricular ejection fraction; FS - fractional shortening; DOE - Dyspnea on exertion, PND - Paroxysmal nocturnal dyspnea, DCM - Dilated cardiomyopathy, PVC - Premature ventricular contractions, LBBB - Left bundle branch block, CHF - Congestive heart failure, SD - Sudden death, NSVT - Non-sustained ventricular tachycardia, PM - Pace maker, RBBB - Right bundle branch block, AF - Atrial fibrillation, AVB - 1st degree atrio-ventricular block, LAFB - Left anterior fascicular block, SSS - sick sinus syndrome.</p

Venn diagram reflecting variant overlap between and among patients.

<p>A Venn diagram depicts the number of variants after bioinformatics filtering to identify nonsynonymous, nonsense and splice site variants that were located in conserved regions (by ANNOVAR), novel (absent in 1000 Genomes and NHLBI Exome Sequencing Project datasets), and were predicted to be damaging by in silico analyses. The numbers and overlap regions in the Venn diagram show the variants unique to or shared among three individuals (IV:4, IV:7, and IV:14) from family AD-FDC1.</p

Pedigrees of families (A) AD-FDC1 and (B) AD-FDC27.

<p>The family structures of both TNNT2 mutation families are shown. The proband is indicated by an arrow. Males and females are depicted as squares and circles, respectively. Affected individuals are identified by shading. Presence or absence of the Arg173Trp variant confirmed by Sanger sequencing is indicated by plus (‘+’) and minus (‘−’) signs, respectively. Paired numbers beneath individuals represent the numbered haplotypes according to (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078104#pone-0078104-t004" target="_blank">Table 4</a>); double-numbers represent recombinant haplotypes further detailed in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078104#pone.0078104.s003" target="_blank">Table S3</a>. Individuals studied by exome sequencing are indicated by present of black underline beneath haplotype numbering.</p

Hap Map project haplotypes and population frequencies of Utah residents with northern and western European ancestry (CEU).

<p>The TNNT2, Arg173Trp variant (Chr1∶201,332,477) was present on separate haplotype, segregating with haplotypes #2 and #1 in families AD-FDC1 and AD-FDC27, respectively.</p

Resultant variants and dbNSFP scores after bioinformatic filtering in AD-FDC1.

<p>Shown are the six genes containing exome-detected variants present in all three subjects tested. The Genebank NM number, chromosome and nucleotide position are shown along with the predicted consequence of each variant. Only the TNNT2 variant segregates with the disease phenotype in AD-FDC1. SIFT, Polyphen2, LRT, and MutationTaster scores derived from dbNSFP are presented. SIFT scores less than 0.05 are predicted to be damaging, otherwise they are predicted to be tolerated. Polyphen2_HDIV_scores range from 0 to 1. Scores in the range of 0.957 to 1 are predicted to be possibly damaging and those in the range of 0.453 to 0.956 are predicted to be benign. Polyphen2_HVAR_scores range from 0 to 1. Scores in the range of 0.909 to1 are predicted to be possibly damaging and scores in the range of 0.447 to 0.908 are predicted to be benign. Lower LRT p-values correspond to predictions that are more damaging. A MutationTaster value close to 1 indicates a high ‘security’ of the prediction.</p

Supplemental Material for Baschal et al., 2018

<p>Idiopathic scoliosis (IS) is a complex genetic disease of unknown etiology. We completed exome sequencing for five IS families and performed GO term enrichment analyses on the resulting variant lists. Overall, we identified enriched categories in our affected families that include stereocilia and other actin-based cellular projections, cilia and other microtubule-based cellular projections, and the extracellular matrix (ECM). Our results suggest that there are multiple paths to IS and provide a foundation for future studies of IS pathogenesis.</p><p></p