Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection.

Although human induced pluripotent stem cell (hiPSC) lines are karyotypically normal, they retain the potential for mutation in the genome. Accordingly, intensive and relevant quality controls for clinicalgrade hiPSCs remain imperative. As a conceptual approach, we performed RNA-seq-based broad-range genetic quality tests on GMp-compliant human leucocyte antigen (HLA)-homozygous hipScs and their derivatives under postdistribution conditions to investigate whether sequencing data could provide a basis for future quality control. We found differences in the degree of single-nucleotide polymorphism (SNP) occurring in cells cultured at three collaborating institutes. However, the cells cultured at each centre showed similar trends, in which more SNPs occurred in late-passage hiPSCs than in earlypassage hiPSCs after differentiation. In eSNP karyotyping analysis, none of the predicted copy number variations (CNVs) were identified, which confirmed the results of SNP chip-based CNV analysis. HLA genotyping analysis revealed that each cell line was homozygous for HLA-A, HLA-B, and DRB1 and heterozygous for HLA-DPB type. Gene expression profiling showed a similar differentiation ability of early-and late-passage hiPSCs into cardiomyocyte-like, hepatic-like, and neuronal cell types. However, time-course analysis identified five clusters showing different patterns of gene expression, which were mainly related to the immune response. In conclusion, RNA-seq analysis appears to offer an informative genetic quality testing approach for such cell types and allows the early screening of candidate hipSc seed stocks for clinical use by facilitating safety and potential risk evaluation.In the decades since the discovery of human induced pluripotent stem cells (hiPSCs) by Takahashi and Yamanaka 1 , considerable advances have been made in our understanding of these cells 2-4 . hiPSCs currently present potential clinical applications in cell therapy and regenerative medicine 5 , and with the broadening of these clinical applications, the standardization of the quality control (QC) of hiPSCs is becoming increasingly open Scientific RepoRtS | (2020) 10:3939 | https://doi.org/10.1038/s41598-020-60466-9www.nature.com/scientificreports www.nature.com/scientificreports/ important. In particular, the evaluation of the genetic stability of the starting materials and the final product is a key consideration during QC processes for selecting suitable hiPSC lines for clinical application, as it may affect final product quality, efficacy, and safety 6,7 .The genomes of hiPSCs are characterized by potentially wide variability, including aneuploidy, subchromosomal copy number variation (CNV), single-nucleotide variations (SNVs), and epigenetic aberrations 8 . Deletions of tumour suppressor genes and changes in immune response-related genes may not be reflected in phenotypic changes in hiPSCs; however, they could play a pivotal role once the cells have differentiated or been transplanted, although such mutations are also known to occur in perfectly he...

BackgroundMultiple endocrine neoplasia type 1 (MEN1) syndrome is an autosomal dominant hereditary disorder characterized by the presence of endocrine tumors affecting the parathyroid, pancreas, and pituitary. A heterozygous germline inactivating mutation in the MEN1 gene (first hit) may be followed by somatic loss of the remaining normal copy or somatic mutations in the MEN1 gene (second hit). Whole-exome sequencing has been successfully used to elucidate the mutations associated with the different types of tumors.Case presentationWe performed whole-exome sequencing (WES) on three parathyroid tumors, one pancreatic insulinoma, and a blood sample taken from the same patient with MEN1 to study tumor heterogeneity in MEN1 originating from different tumors. We identified a novel frame-shift deletion (c.1382_1383delAG, p.E461GfsX69) in the MEN1 gene using WES, which was confirmed by Sanger sequencing. WES and the SNP array revealed somatic LOH on chromosome 11 in parathyroid tumors (left upper, left lower, and right upper parathyroid). However, we did not detect a somatic MEN1 gene mutation or LOH in the pancreatic insulinoma. WES revealed two somatic functional variants outside the MEN1 gene in the pancreatic insulinoma.ConclusionsThis study revealed heterogeneity among tumors in the same patient with MEN1, suggesting that different tumor-specific tumorigenic mechanisms may contribute to the pathogenesis of MEN1 tumors. The present study supports the clinical applicability of the WES strategy to research on multiple tumor samples and blood.Electronic supplementary materialThe online version of this article (10.1186/s12881-017-0465-9) contains supplementary material, which is available to authorized users.