Comparative evaluation of the heterozygous variant standard deviation as a quality measure for next-generation sequencing.

Next-generation sequencing holds unprecedented throughput in terms of informational content to cost. The technology has entered the scene in laboratory diagnostics and offers flexible workflows in biomedical research. However, the rapid acquisition of genomic data also gives rise to a substantial fraction of sequencing artifacts, causing the detection of false-positive germline variants or erroneous somatic mutations. Consequently, there is a pressing need for efficient and practical quality assessment in sequencing projects. In this study, we investigate using heterozygous variant allele frequency (VAF) standard deviation (σ) for supplementary quality control. Whereas several proposed quality metrics are based on empirical assessments, the dispersion of the allele frequencies reflects a direct approximation of the inherent and discrete features of a diploid genome. Consequently, homologous chromosomes display heterozygous VAF of approximately 1/2. Based on the meta-analysis of 152 whole-exome sequencing data sets, we found that σ reflects both sequencing coverage and noise and can be effectively modeled. It is concluded that the relative comparison of heterozygous VAF σ provides a practical handle for quality assessment, even for samples afflicted with copy-number alterations. The approach can be implemented when performing whole-exome, whole-genome, or targeted panel sequencing and helps identify problematic samples, such as those retrieved from archived formalin-fixed paraffin-embedded tissue.

Detailed characterization of the transcriptome of single B cells in mantle cell lymphoma suggesting a potential use for SOX4.

Mantle cell lymphoma (MCL) is a malignancy arising from naive B lymphocytes with common bone marrow (BM) involvement. Although t(11;14) is a primary event in MCL development, the highly diverse molecular etiology and causal genomic events are still being explored. We investigated the transcriptome of CD19+ BM cells from eight MCL patients at single-cell level. The transcriptomes revealed marked heterogeneity across patients, while general homogeneity and clonal continuity was observed within the patients with no clear evidence of subclonal involvement. All patients were SOX11+CCND1+CD20+. Despite monotypic surface immunoglobulin (Ig) κ or λ protein expression in MCL, 10.9% of the SOX11 + malignant cells expressed both light chain transcripts. The early lymphocyte transcription factor SOX4 was expressed in a fraction of SOX11 + cells in two patients and co-expressed with the precursor lymphoblastic marker, FAT1, in a blastoid case, suggesting a potential prognostic role. Additionally, SOX4 was found to identify non-malignant SOX11- pro-/pre-B cell populations. Altogether, the observed expression of markers such as SOX4, CD27, IgA and IgG in the SOX11+ MCL cells, may suggest that the malignant cells are not fixed in the differentiation state of naïve mature B cells, but instead the patients carry B lymphocytes of different differentiation stages.