Search

Additional file 1: Table S1. Primer sequences for amplification of coding exonic regions of the CDH1 gene.

Clinical details, pathologic work-up, and sequencing methodology used in the current study. Figure S1. Additional histopathology from case #1 showed characteristic eosinophilic granular bodies (EGBs) (a) and an elevated proliferation index (Ki-67) (b). Immunohistochemistry for p16 showed loss of expression in tumor cells with retained expression in non-neoplastic cells (c, arrowhead), consistent with deletion of the INK4a locus. Staining with mutant-specific BRAF (VE1) was negative (d). Figure S2. Case #2 showed lipidized tumor cells and PAS-positive, diastase-resistant EGBs (arrowheads) (a). Nuclear pleomorphism and increased mitotic activity were seen (b, c). Neurofilament stain showing circumscription of the tumor mass (d). BRAF V600E was negative by IHC (e). Figure S3. MI-ONCOSEQ integrative sequencing report elements: somatic point mutations for case #1 (a) and #2 (c). Copy number plots for case #1 (b) and #2 (d). (DOCX 13229 kb)

Clinical details, pathologic work-up, and sequencing methodology used in the current study. Figure S1. Additional histopathology from case #1 showed characteristic eosinophilic granular bodies (EGBs) (a) and an elevated proliferation index (Ki-67) (b). Immunohistochemistry for p16 showed loss of expression in tumor cells with retained expression in non-neoplastic cells (c, arrowhead), consistent with deletion of the INK4a locus. Staining with mutant-specific BRAF (VE1) was negative (d). Figure S2. Case #2 showed lipidized tumor cells and PAS-positive, diastase-resistant EGBs (arrowheads) (a). Nuclear pleomorphism and increased mitotic activity were seen (b, c). Neurofilament stain showing circumscription of the tumor mass (d). BRAF V600E was negative by IHC (e). Figure S3. MI-ONCOSEQ integrative sequencing report elements: somatic point mutations for case #1 (a) and #2 (c). Copy number plots for case #1 (b) and #2 (d). (DOCX 13229 kb)

Appendix 1. Antibodies used for immunohistochemistry. Histopathological examination using fresh frozen muscle biopsy specimen from the patient was performed using the immunostains for: MHC1, Lamin A/C, C5b9, CD163/CD4, CD3/CD20. The antibodies used and respective protocols are shown. Appendix 2 Sanger sequencing chromatogram completed by a CLIA certified laboratory. Data from Sanger sequencing was used to confirm the patient’s whole exome sequencing (WES) results. Similar to the WES data, Sanger sequencing chromatogram revealed a heterozygous c.29 C > T mutation in exon 1. In the figure, both the wild type and the patient’s data with this mutation are shown. (PDF 618 kb)

Appendix 1. Antibodies used for immunohistochemistry. Histopathological examination using fresh frozen muscle biopsy specimen from the patient was performed using the immunostains for: MHC1, Lamin A/C, C5b9, CD163/CD4, CD3/CD20. The antibodies used and respective protocols are shown. Appendix 2 Sanger sequencing chromatogram completed by a CLIA certified laboratory. Data from Sanger sequencing was used to confirm the patient’s whole exome sequencing (WES) results. Similar to the WES data, Sanger sequencing chromatogram revealed a heterozygous c.29 C > T mutation in exon 1. In the figure, both the wild type and the patient’s data with this mutation are shown. (PDF 618 kb)