ArCH: Improving the performance of clonal hematopoiesis variant calling and interpretation

MOTIVATION: The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. The lack of well-validated bioinformatic pipelines for CH calling may contribute to lack of reproducibility in studies of CH. RESULTS: Here, we developed ArCH, an Artifact filtering Clonal Hematopoiesis variant calling pipeline for detecting single nucleotide variants and short insertions/deletions by combining the output of four variant calling tools and filtering based on variant characteristics and sequencing error rate estimation. ArCH is an end-to-end cloud-based pipeline optimized to accept a variety of inputs with customizable parameters adaptable to multiple sequencing technologies, research questions, and datasets. Using deep targeted sequencing data generated from six acute myeloid leukemia patient tumor: normal dilutions, 31 blood samples with orthogonal validation, and 26 blood samples with technical replicates, we show that ArCH improves the sensitivity and positive predictive value of CH variant detection at low allele frequencies compared to standard application of commonly used variant calling approaches. AVAILABILITY AND IMPLEMENTATION: The code for this workflow is available at: https://github.com/kbolton-lab/ArCH

Assessment of neutralizing antibody responses after natural SARS-CoV-2 infection and vaccination in congolese individuals

Abstract Background Assessing immune responses after vaccination is part of the evaluation package of vaccine effectiveness in the real world. Regarding SARS-CoV-2, neutralizing antibody levels has been shown to be a good indicator of antibody immune response boosting. So far, limited data have been reported from Africa including in Central Africa. The objective of this study was to provide data on anti-S1 spike total IgG and neutralizing antibodies in vaccinated and non-vaccinated including naturally infected Congolese population during B.1.214.1 and B.1.617.2 variant waves. Methods Recruited patients were divided into 4 groups: (1) Naturally infected by the B.1.214.1 variant on January 2021 and followed up until September 2021. These patients have been vaccinated at month 07 and then followed up for 2 months post vaccination; (2) Naturally infected by the B.1.617.2 variant from June 2021; (3) unvaccinated SARS-CoV-2 individuals with no history of prior SARS-CoV-2 infection; (4) fully vaccinated individuals with sinopharm/BBIP-CorV or Janssen/Ad26.COV2.S. SARS-CoV-2 was detected by qRT-PCR and sequenced using Next-Generation Sequencing. ELISA method was used for detecting IgG, and neutralizing Antibody against SARS-CoV-2 antigens using commercial neutralizing assay. Results Individuals infected by the B.1214.1 variant elicited consistently high IgG titers at 02, 03 and 06 months. Two months post vaccination with BBIP-CorV, participants showed a significant increase by × 2.5 fold (p < 0.0001) of total IgG and X1.5 fold for neutralizing antibody capacity. This study showed that natural infection with B1.617.2 (delta) variant was more immunogenic compared to those being infected with B1.214.2 variant. We found a significantly higher concentration in anti-SARS-CoV-2 IgG (p < 0.0002) and antibodies neutralization capacity (P < 0.0001) in fully vaccinated compared to unvaccinated participants. Two months post vaccination, individuals who received Janssen/Ad26.COV2.S presented higher (p = 0.01) total IgG to spike protein compared to BBIP-CorV. Conclusion Both natural infection and vaccination with BBIP-CorV and Janssen/Ad26.COV2.S induced antibody response in Congolese population. In addition, Janssen/Ad26.COV2.S was more immunogenic than Sinopharm/BBIP-CorV. There is a need to investigate the duration of these antibodies both in previously infected and naive vaccinated Congolese to allow public heath stakeholders to make evidence-based decision on vaccine schedule for the Congolese population