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Thursday, August 27, 2020

Certified Service Provider Profile: GATC Biotech expands applications with unique attributes of SMRT Sequencing

GATC Biotech, the first PacBio Certified Service Provider in Europe, became a leader in the sequencing field by continuously adopting new technologies, developing innovative products, and delivering quality results to its 10,000-strong customer base. Today, GATC Biotech is constantly looking for new ways to maximize the value of highly accurate, long-read sequencing.

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Thursday, August 27, 2020

Case Study: SMRT sequencing brings clarity to HIV vaccine and transplant research at the Wisconsin national primate research center

The Wisconsin National Primate Research Center (WNPRC) is a leading Major Histocompatibility Complex (MHC) typing lab that focuses on monkeys. While many scientists are familiar with the importance of characterizing the histocompatibility region of the human genome for applications like disease research or tissue typing before organ transplantation, fewer are aware of the need to accurately type this region in non-human primates. At the primate research lab, part of the University of Wisconsin- Madison, scientists are analyzing immune regions to help test potential HIV vaccines and AIDS therapies. Their work is essential for understanding the effects of treatment ahead of…

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Thursday, August 27, 2020

Product Note: Fast, high-resolution DNA sizing with the fragment analyzer system

The Agilent 5200, 5300, and 5400 Fragment Analyzer instruments are fast, high-resolution benchtop capillary electrophoresis (CE) platforms that utilize proprietary markers to accurately size fragments ranging from 10 to 50 kb. This platform allows important DNA quality checkpoints to be completed in one hour for de novo large-genome sequencing projects and other PacBio applications leveraging multi-kilobase read lengths. The instrument can be used in place of time-consuming QC steps involving pulsed field gel electrophoresis (PFGE), saving time by avoiding multiple overnight gel runs when preparing large-insert SMRTbell libraries. Alternative DNA-sizing instruments cannot accurately resolve large DNA fragments in this range.

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Thursday, August 27, 2020

Product Note: Fast, high-resolution DNA sizing with the Agilent Femto Pulse system

The Agilent Femto Pulse system automated pulsed-field CE instrument is a fast, high-resolution benchtop capillary electrophoresis (CE) platform that utilizes pulsed-field electrophoresis to separate high molecular weight DNA fragments. This platform allows important DNA quality checkpoints to be completed in less than 1.5 hours with minimal sample input for de novo large genome sequencing projects and other PacBio applications leveraging multi-kilobase read lengths. The instrument can be used in place of gel-based pulsed-field electrophoresis (PFGE) systems to fully support generation of large-insert SMRTbell libraries with accurate sizing to 165 kb. Alternative DNA sizing instruments cannot accurately resolve large DNA fragments…

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Tuesday, April 21, 2020

Whole-genome sequence of the oriental lung fluke Paragonimus westermani.

Foodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Approximately 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available.We sequenced and assembled the genome of P. westermani, which is among the largest of the known pathogen genomes with an estimated size of 1.1 Gb. A 922.8 Mb genome assembly was generated from Illumina and Pacific Biosciences (PacBio) sequence data, covering 84% of…

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Tuesday, April 21, 2020

Profiling the genome-wide landscape of tandem repeat expansions.

Tandem repeat (TR) expansions have been implicated in dozens of genetic diseases, including Huntington’s Disease, Fragile X Syndrome, and hereditary ataxias. Furthermore, TRs have recently been implicated in a range of complex traits, including gene expression and cancer risk. While the human genome harbors hundreds of thousands of TRs, analysis of TR expansions has been mainly limited to known pathogenic loci. A major challenge is that expanded repeats are beyond the read length of most next-generation sequencing (NGS) datasets and are not profiled by existing genome-wide tools. We present GangSTR, a novel algorithm for genome-wide genotyping of both short and…

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Tuesday, April 21, 2020

Human contamination in bacterial genomes has created thousands of spurious proteins.

Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing…

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Tuesday, April 21, 2020

Long-read sequence and assembly of segmental duplications.

We have developed a computational method based on polyploid phasing of long sequence reads to resolve collapsed regions of segmental duplications within genome assemblies. Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA ) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. We apply it to single-molecule, real-time sequence data from three human genomes and recover 33-79 megabase pairs (Mb) of duplications in which approximately half of the loci are diverged (99.9%) and that the diverged sequence corresponds to copy-number-variable paralogs that…

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Tuesday, April 21, 2020

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.

The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.Each of the assembly steps reduced the number of gaps and incorporated a substantial…

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Monday, March 30, 2020

AGBT Conference: Whole human genome SMRT Sequencing reveals uncharacterized structural variations providing a path to more informed diagnostic testing

In this AGBT talk, Mount Sinai’s Eric Schadt uses PacBio sequencing on human genomes and reports finding uncharacterized structural variation that could have diagnostic utility. Schadt says that SMRT sequencing is advantageous for long-range genetic information, extreme GC content, and highly repetitive regions. He presents sequence data for a CEPH individual studied for repeat expansions, showing that long reads can resolve the majority of these regions.

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Monday, March 30, 2020

AGBT Conference: Evolving approaches to reference assembly improvement

Valerie Schneider speaks about Genome Reference Consortium efforts to improve assembly of the human reference genome. SMRT Sequencing has been useful for resolving some highly repetitive regions, like the mucin genes. Haploid assemblies produced with long-read sequencing are also making complex regions more tractable.

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