System analysis of the sequencing quality of human whole exome samples on BGI NGS platform

Belova, Vera; Pavlova, Anna; Afasizhev, Robert; Moskalenko, Viktoriya; Korzhanova, Margarita; Krivoy, Andrey; Cheranev, Valery; Nikashin, Boris; Bulusheva, Irina; Rebrikov, Denis; Korostin, Dmitriy

doi:10.1038/s41598-021-04526-8

Cited by 12 publications

(12 citation statements)

References 30 publications

(37 reference statements)

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“…The amount of raw sequencing reads was designed to achieve 100X unique coverage of the exome region. The data pre-processing processes were conducted as previously described ( Cao et al, 2020 ; Belova et al, 2022 ). Briefly, first low-quality sequencing raw reads were filtered by SOAPnuke v1.5.6 (-Q 2 -G), and then high-quality reads were mapped to human reference genome GRCh37 (hg19) with the BWA-mem algorithm of BWA v0.7.17 (-R “@RG\tID:SampleID\tSM:SampleName\tPL: COMPLETE” -t 2).…”

Section: Methodsmentioning

confidence: 99%

Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease

et al. 2022

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Congenital heart disease (CHD) is the most common congenital malformation in fetuses and neonates, which also represents a leading cause of mortality. Although significant progress has been made by emerging advanced technologies in genetic etiology diagnosis, the causative genetic mechanisms behind CHD remain poorly understood and more than half of CHD patients lack a genetic diagnosis. Unlike carefully designed large case-control cohorts by multicenter trials, we designed a reliable strategy to analyze case-only cohorts to utilize clinical samples sufficiently. Combined low-coverage whole-genome sequencing (WGS) and whole-exome sequencing (WES) were simultaneously conducted in a patient-only cohort for identifying genetic etiologies and exploring candidate, or potential causative CHD-related genes. A total of 121 sporadic CHD patients were recruited and 34.71% (95% CI, 26.80 to 43.56) was diagnosed with genetic etiologies by low-coverage WGS and WES. Chromosomal abnormalities and damaging variants of CHD-related genes could explain 24.79% (95% CI, 17.92 to 33.22) and 18.18% (95% CI, 12.26 to 26.06) of CHD patients, separately, and 8.26% (95% CI, 4.39 to 14.70) of them have simultaneously detected two types of variants. Deletion of chromosome 22q11.2 and pathogenic variants of the COL3A1 gene were the most common recurrent variants of chromosomal abnormalities and gene variants, respectively. By in-depth manual interpretation, we identified eight candidate CHD-causing genes. Based on rare disease-causing variants prediction and interaction analysis with definitive CHD association genes, we proposed 86 genes as potential CHD-related genes. Gene Ontology (GO) enrichment analysis of the 86 genes revealed regulation-related processes were significantly enriched and processes response to regulation of muscle adaptation might be one of the underlying molecular mechanisms of CHD. Our findings and results provide new insights into research strategies and underlying mechanisms of CHD.

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Section: Methodsmentioning

confidence: 99%

Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease

et al. 2022

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“…DNA was fragmented to an average fragment length of 250 bp on a Covaris S-220 device (Covaris, Woburn, MA, USA). DNA enrichment was carried out on preliminary pooled libraries [ 48 ] using SureSelect Human All Exon v7 probes, recognizing the complete human genome (Agilent, Santa Clara, CA, USA). The libraries were circularized and sequenced in paired-end mode on the MGISEQ-2000 platform using the DNBSEQ-G400RS High-throughput Sequencing Set PE100 according to the manufacturer’s protocol (MGI Tech), with an average coverage of 100x.…”

Section: Methodsmentioning

confidence: 99%

Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy

Semchenkova

Mikhailova

Komkov

et al. 2022

IJMS

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We report incidence and deep molecular characteristics of lineage switch in 182 pediatric patients affected by B-cell precursor acute lymphoblastic leukemia (BCP-ALL), who were treated with blinatumomab. We documented six cases of lineage switch that occurred after or during blinatumomab exposure. Therefore, lineage conversion was found in 17.4% of all resistance cases (4/27) and 3.2% of relapses (2/63). Half of patients switched completely from BCP-ALL to CD19-negative acute myeloid leukemia, others retained CD19-positive B-blasts and acquired an additional CD19-negative blast population: myeloid or unclassifiable. Five patients had KMT2A gene rearrangements; one had TCF3::ZNF384 translocation. The presented cases showed consistency of gene rearrangements and fusion transcripts across initially diagnosed leukemia and lineage switch. In two of six patients, the clonal architecture assessed by IG/TR gene rearrangements was stable, while in others, loss of clones or gain of new clones was noted. KMT2A-r patients demonstrated very few additional mutations, while in the TCF3::ZNF384 case, lineage switch was accompanied by a large set of additional mutations. The immunophenotype of an existing leukemia sometimes changes via different mechanisms and with different additional molecular changes. Careful investigation of all BM compartments together with all molecular –minimal residual disease studies can lead to reliable identification of lineage switch.

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“…Previously pooled DNA libraries were enriched following the RSMU_exome protocol (12). 20 DNA libraries were divided into 2 pools each containing 10 libraries.…”

Section: Methodsmentioning

confidence: 99%

“…We prepared 20 libraries, divided them into 2 pools of 10 libraries and performed 2 rounds of enrichment of the pools using the v7 or v8 probes following the RSMU_exome protocol (12). The sequenced pools were compared using bioinformatics pipeline based on the following characteristics: target regions, the percentages of on-targets, off-targets, and duplicates as well depth of coverage of the regions with various GC content.…”

Section: Introductionmentioning

confidence: 99%

Performance Comparison Of Agilent New SureSelect All Exon v8 Probes With v7 Probes For Exome Sequencing

Belova

Shmitko

Pavlova

et al. 2022

Preprint

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Exome sequencing may become routine in health care it increases the chance of pinpointing the genetic cause of an individual patient’s condition and thus making an accurate diagnosis. It is important for facilities providing genetic services to keep track of changes in the technology of exome capture in order to maximize throughput while reducing cost per sample. In this study, we focused on comparing the newly released exome probe set Agilent SureSelect Human All Exon v8 and the previous probe set v7. In preparation for higher throughput of exome sequencing using the DNBSEQ-G400, we evaluated target design, coverage statistics, and variants across these two different exome capture products. Although the target size of the v8 design has not changed much compared to the v7 design (35.24 Mb vs 35.8 Mb), the v8 probe design allows you to call more of SNVs (+3.06%) and indels (+8.49%) with the same number of raw reads per sample on the common target regions (34.84 Mb). Our results suggest that the new Agilent v8 probe set for exome sequencing yields better data quality than the current Agilent v7 set.

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System analysis of the sequencing quality of human whole exome samples on BGI NGS platform

Cited by 12 publications

References 30 publications

Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease

Genetic Diagnostic Yield and Novel Causal Genes of Congenital Heart Disease

Lineage Conversion in Pediatric B-Cell Precursor Acute Leukemia under Blinatumomab Therapy

Performance Comparison Of Agilent New SureSelect All Exon v8 Probes With v7 Probes For Exome Sequencing

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