Description of the novel HLA-C allele, HLA-C*12:376, identified in a deceased COVID-19 patient

The new allele HLA-C*12:376 showed one nonsynonymous nucleotide difference compared with the C*12:03:01:01 allele in codon 30.

Description of the novel allele HLA-B*07:473, identified in a bone marrow donor

The new HLA-B*07:473 allele showed two nonsynonymous nucleotide differences compared with the HLA-B*07:02:01:01 allele in codon 116.

Performance comparison of Agilent new SureSelect All Exon v8 probes with v7 probes for exome sequencing

Exome sequencing is becoming a routine in health care, because 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.

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

Human exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia. The reliability and quality of the obtained data are already beyond any doubt. However, only a few kits compatible with these sequencers can be used for such specific tasks as exome sequencing. We developed our own solution for library pre-capture pooling and exome enrichment with Agilent probes. In this work, using a set of the standard benchmark samples from the Platinum Genome collection, we demonstrate that the qualitative and quantitative parameters of our protocol which we called "RSMU_exome" exceed those of the MGI Tech kit. Our protocol allows for identifying more SNV and indels, generates fewer PCR duplicates, enables pooling of more samples in a single enrichment procedure, and requires less raw data to obtain results comparable with the MGI Tech's protocol. The cost of our protocol is also lower than that of MGI Tech's solution.

Description of a novel allele HLA-DRB1*16:02:10, identified in a bone marrow donor

The new allele HLA-DRB1*16:02:10 showed one synonymous nucleotide difference with HLA-DRB1*16:02:01:01 in codon 58.

The novel HLA-DQB1*05:02:24 allele, identified in a Russian bone marrow donor

The new allele HLA-DQB1*05:02:24 showed one synonymous nucleotide difference with HLA-DQB1*05:02:01:01 in codon 140.

A novel allele, HLA-C*15:227, identified when typing COVID-19 patients

HLA‐C*15:227 differs from HLA‐C*15:02:01:01 by a single nonsynonymous change (368A → G Tyrosine 99 to Cysteine).

HLA-A*11:382N, a novel HLA-A null allele identified by next-generation sequencing

The new allele HLA-A*11:382N showed one nucleotide difference with HLA-A*11:01:01:01 at codon 254 (nonsense mutation).

HLA-C*06:287, a novel HLA-C*06 allele identified by sequence-based typing

The new allele HLA-C*06:287 showed one nucleotide difference with HLA-C*06:02:01:01 at codon 219 (CGG/CAG).

Description of a novel HLA-A allele, HLA-A*03:365, identified in a bone marrow donor from Russia

The novel allele HLA-A*03:365 showed a single nucleotide difference from A*03:01:01:01 where 135 Alanine is changed to Proline.