Powering genetic discovery
Advanced exploration of human genomes requires reference quality assemblies of diverse populations. We must look beyond single nucleotides to include comprehensive structural variant mapping of individuals and large cohorts to fully understand the complexity of human health and disease.
A world of diversity coming to light
Single Molecule, Real-Time (SMRT) Sequencing is informing population-specific reference genomes around the world by uncovering regions of the genome not previously sequenced and enabling detection of all variant types. With the PacBio System scientists can:
- Generate de novo assemblies of population-specific reference genomes
- Utilize low-coverage, long-read whole genome sequencing to detect structural variants
- Conduct targeted sequencing for novel allele-discovery for genes of interest
Spotlight: Structural variant discovery with PacBio long-read sequencing
Explore human genetic variation and learn how SMRT Sequencing uncovers the full spectrum of structural variants to advance understanding of genetic disease and broaden our knowledge of human diversity.
Infographic: Structural Variants and Disease
Explore the types of human genomic variation and the diseases known to be caused by structural variants.
Whitepaper: Structural variation in the human genome
Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution, and genetic diversity.
Structural Variation Project Calculator
Use this calculator to estimate the time and materials needed for structural variant discovery on the Sequel System.
Spotlight: SMRT Sequencing delivers a Chinese reference genome
Scientists used PacBio long-read sequencing to construct a de novo assembly of a Chinese genome (HX-1). This high-quality assembly filled 247 N-gaps in the GRCh38 reference sequence and shed light on 12.8 Mb of Chinese population-specific sequences and novel structural variants. Explore this research further:
Shi, L. et al., 2016. Long-read sequencing and de novo assembly of a Chinese genome. Nature Communications, 7, p.12065.
Spotlight: Long-read sequencing sheds light on MHC diversity in Africa
Martin Pollard presents his research to better represent natural variation in the major histocompatibility complex (MHC) among African populations. PacBio long reads provided full-length sequences of the human leukocyte antigen haplotypes, enabling improved understanding of genetic diversity.
Pollard, M., 2016. ASHG Virtual Poster: The MHC Diversity in Africa Project (MDAP) pilot – 125 African high-resolution HLA types from 5 populations. 66th Annual Meeting of the American Society of Human Genetics.
For more information about how SMRT Sequencing can advance your population genetics research, contact us.
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- Nakano, Kazuma et al. (2017) Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Human Cell
- Merker, Jason D et al. (2017) Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in Medicine
- Roe, David et al. (2017) Revealing complete complex KIR haplotypes phased by long-read sequencing technology bioRxiv
- Koren, Sergey et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research
- Huddleston, John et al. (2017) Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Research
- Seo, Jeong-Sun et al. (2016) De novo assembly and phasing of a Korean human genome. Nature
- Suzuki, Yuta et al. (2016) AgIn: Measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics
- Ashley, Euan A et al. (2016) Towards precision medicine. Nature Reviews. Genetics
- Steinberg, Karyn Meltz et al. (2016) High-quality assembly of an individual of Yoruban descent bioRxiv
- Shi, Lingling et al. (2016) Long-read sequencing and de novo assembly of a Chinese genome. Nature Communications
- Huddleston, John et al. (2016) An incomplete understanding of human genetic variation. Genetics
- Chaisson, Mark J P et al. (2015) Genetic variation and the de novo assembly of human genomes. Nature Reviews. Genetics
- Pendleton, Matthew et al. (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods
- Editorial et al. (2015) Whole genome? Nature Genetics
- Berlin, Konstantin et al. (2015) Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology
- English, Adam C et al. (2015) Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics
- Chaisson, Mark J P et al. (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature
- Huddleston, John et al. (2014) Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research
- Schneider, Valerie A et al. (2017) Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Research
- Novak, Adam M et al. (2017) Genome graphs bioRxiv
- Kojima, Kaname et al. (2016) STR-realigner: a realignment method for short tandem repeat regions. BMC Genomics
- Cho, Yun Sung et al. (2016) An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature Communications
- Liljegren, Mikkel Meyn et al. (2016) Microsatellite length scoring by Single Molecule Real Time Sequencing – Effects of sequence structure and PCR regime. PLoS One
- Garg, Shilpa et al. (2016) Read-based phasing of related individuals bioRxiv
- Poster: Hickey, L. et al. (2017) Detecting pathogenic structural variants with low-coverage PacBio sequencing.
- Poster: Wenger, Aaron et al. (2017) Structural variant detection with low-coverage Pacbio sequencing
- Poster: Watson, C. T. et al. (2016) Characterizing haplotype diversity at the immunoglobulin heavy chain locus across human populations using novel long-read sequencing and assembly approaches
- Poster: Wenger, A. et al. (2016) Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Poster: Carroll, A. et al. (2016) Structural variant combining Illumina and low-coverage PacBio
- Poster: Pollard, M. O. et al. (2016) The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- (2017) Video: Discover structural variation with long-read sequencing
- Wenger, Aaron (2017) Webinar: Detecting Structural Variants in PacBio Reads – Tools and Applications
- (2017) Tutorial: Minor Variant Analysis
- (2017) Tutorial: Structural Variant Calling
- Wenger, Aaron (2017) Webinar: Structural Variant Detection in SMRT Link 5 with PBSV
- Korlach, Jonas (2017) AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs
- Schatz, Michael (2017) AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples
- Korlach, Jonas (2016) ASHG PacBio Workshop: A future of high-quality genomes, transcriptomes, and epigenomes
- Wenger, A. and Kujawa, S. and Hickey, L. and Chin, J. and Korlach, J. (2016) ASHG Virtual Poster: Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads
- Pollard, Martin (2016) ASHG Virtual Poster: The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations
- Laird Smith, Melissa (2016) Nature Webinar: Using long-read sequencing to characterize population diversity at the immunoglobulin heavy chain locus
- Carroll, Andrew (2016) DNAnexus Webinar: Accurate calling of structural variation in PacBio data
- Meltz Steinberg, Karyn (2016) AGBT Conference: The first African reference genome assembly
- Ameur, Adam (2016) AGBT Roche and PacBio Workshop: Clinical SMRT Sequencing – from single genes to complete genomes
- Ashley, Euan (2016) AGBT Roche and PacBio Workshop: Towards precision medicine
- Schatz, Michael (2016) PAG Conference: Analysis of structural variants using 3rd generation sequencing
- Hunkapiller, Michael and Venter, J. Craig and Myers, Gene and Church, Deana and Seo, Jeong-Sun and McCombie, W. Richard (2015) AGBT PacBio Workshop: Full workshop recording
- Venter, Craig (2015) AGBT PacBio Workshop: The human genome – from one to one million
- Infographic: Structural Variants and Disease (2017)
- Application Brief: Low-coverage, long-read whole genome sequencing for structural variation – Best Practices. (2017)
- PacBio Certified Service Providers (2017)
- Human Biomedical Research Brochure: The most comprehensive view of the human genome (2017)
- Case Study: Improving precision medicine studies in Asia using ethnicity-specific human reference genomes and PacBio long-read sequencing. (2017)
- SV Application Brochure: Track the full extent of structural variation in a genome. (2016)