Human genomics

Uncompromising power to unlock the genome to improve human health

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HUMAN GENOMICS SOLUTIONS

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RARE DISEASE

Improve rare disease research efforts with HiFi sequencing to unlock the biology of rare disease that is inaccessible through other technologies.

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PHARMACOGENOMICS

Drive personalized approaches to medicine and care with high resolution insights into medication response, adverse drug reactions, and decreased efficacy.

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NEUROGENOMICS

Identify the genetic drivers of neurological, neuromuscular, and neurodegenerative disorders.

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HLA

Achieve complete and deep full gene HLA profiling without fragmentation. Identify true HLA allelic diversity for improved transplantation and immunological research.

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INTRODUCTION TO HUMAN GENOMICS

PacBio is a global leader in DNA and RNA sequencing, providing the highest accuracy and most comprehensive view of the genome to empower scientists to explore the full spectrum of human genetic variation.

Our technology supports academic centers, for-profit labs, and government institutions around the world focused on:

  • Rare and inherited diseases
  • Pharmacogenomics
  • Carrier screening
  • HLA
  • Complex disease research
  • Inherited cancer risk
  • Epigenetics
  • Transcription + alternative splicing

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UNCOVERING THE UNSEEN IN HUMAN GENOMIC RESEARCH SEQUENCING

Learn how these new applications will enable you to:

  • More accurately identify human disease-causing tandem repeat changes than ever before with TRGT, PacBio’s all-new software solution for state-of-the-art tandem repeat analysis.
  • More easily and cost-effectively obtain detailed sequences of just the genes you care about at scale, with the power of targeted HiFi sequencing and custom gene panels developed by Twist Bioscience.

HUMAN GENOMICS IN ACTION

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THE COMPLETE SEQUENCE OF A HUMAN GENOME

A landmark study by members of the Telomere-to-Telomere Consortium is the…

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ADVANCING PGX STUDIES OF SLC6A4

With highly accurate variant calling and phasing, SMRT sequencing advances pharmacogenomics…

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FULL-LENGTH RNA SEQUENCING OF ALZHEIMER’S

Long-read mRNA sequencing with the Iso-Seq method is used to sequence an Alzheimer’s…

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EXPLORE

Did you know we have a comprehensive library of articles, reports, papers, and videos related to human genomics?

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SHAPING THE FUTURE

CHILDREN’S MERCY KANSAS CITY FINDS INSIGHTS

Children with complex rare diseases are at the forefront of clinical research discoveries at Children’s Mercy Kansas City. See how scientists are moving beyond microarrays and exomes to enable improved care.

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“The SOLVE-RD team knows that long-read HiFi sequencing is

essential

for discovering the causal elements that have proven elusive with previous approaches.”

— Alexander Hoischen, PhD, Associate Professor for Genomic Technologies and Immuno-Genomics and a member of the SOLVE-RD team at Radboud University Medical Center
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UNLOCK YOUR NEXT GREAT DISCOVERY IN HUMAN GENOMICS

36,000 REASONS TO USE HIFI SEQUENCING

In 2019, scientists at the Mayo Clinic identified 36,794 dark regions in 6,054 gene bodies from pathways important to human health, development, and reproduction based on standard whole-genome short-read sequencing data.1 There are potentially thousands of important regions that can be missed without HiFi sequencing.

 

HIFI SEQUENCING REVEALS THE COMPLETE HUMAN REFERENCE GENOME

The complete, gapless human genome marks a new era of genomics where no region of the genome is beyond your reach. In 2021, PacBio’s HiFi technology was used by the Telomere-to- Telomere (T2T) Consortium to fill in those gaps.

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Sequencing error comparison for HiFi, Illumina and ONT graph - PacBio

ACHIEVE FEWER ERRORS DURING VARIANT DETECTION

PacBio’s HiFi technology was found to have the fewest total errors when compared to other technologies by the PrecisionFDA’s Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.5

 

IDENTIFY INDELS WITH CONFIDENCE 

A 2019 University of Washington study found that insertion-deletion mutations (indels) are routinely missed by short-read next generation sequencing (NGS) and long reads deliver 2.48 times as many structural variants as short reads alone, even “at their maximum capacity.” It is estimated that “at least 48% of deletions and 83% of insertions are routinely missed by the application of multiple short-read-calling algorithms.”2

SEE MORE STRUCTURAL VARIANTS

The 1000 Genomes Project sequenced 32 diverse reference genomes with PacBio technology, resulting in the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data, or 64 assembled haplotypes from 32 genomes. Of the 107,590 structural variants identified, 68% were not discovered with short-read sequencing.4

 

OVERCOME PGX CHALLENGES

Interrogating CYP2D6 using short-read sequencing is challenging because of the degree of variation at the CYP2D6 locus and homology with its pseudogenes. Long-read sequencing can overcome these challenges.6

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1. “Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight” Fryer et al. Genome Biol. 2019 May 20;20(1):97
2. “Genetic Variation, Comparative Genomics, and the Diagnosis of Disease.” Eichler EE. N Engl J Med. 2019;381(1):64-74
3. A complete human genome sequence is close: how scientists filled in the gaps https://www.nature.com/articles/d41586-021-01506-w
4. Ebert, Peter & Audano, Peter & Zhu, Qihui & Rodriguez-Martin, Bernardo & Porubsky, David & Bonder, Marc Jan & Sulovari, Arvis & Ebler, Jana & Zhou, Weichen & Mari, Rebecca & Yilmaz, Feyza & Zhao, Xuefang & Hsieh, PingHsun & Lee, Joyce & Kumar, Sushant & Lin, Jiadong & Rausch, Tobias & Chen, Yu & Ren, Jingwen & Eichler, Evan. (2021). Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 372. eabf7117. 10.1126/science.abf7117.
5. https://precision.fda.gov/challenges/10
6. Yang Y, Botton MR, Scott ER, Scott SA. Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics. 2017 May;18(7):673-685.

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2021: A MONUMENTAL DISCOVERY

The complete sequence of a human genome

A landmark study by members of the Telomere-to-Telomere Consortium is the first fully complete assembly to be produced 20 years after the initial drafts of the human genome.

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APPLICATIONS TO FUEL HUMAN GENOMICS RESEARCH

WHOLE GENOME SEQUENCING

Generate complete and phased human genome assemblies of diverse populations to better understand the complexity of health and disease.

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RNA SEQUENCING

Bring certainty to isoform detection with long-read sequencing to decipher how genomic variants drive the phenotypic differences between health and disease.

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TARGETED SEQUENCING

Accurately detect and uncover all variant types even in hard-to-reach regions of the genome.

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STRUCTURAL VARIANT DETECTION

Resolve variants at every scale to improve the power to link genetics to phenotypes of interest for novel discovery of genes and causative variants.

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Human genomics — how PacBio HiFi sequencing compares

PacBio HiFi Illumina Oxford Nanopore
Average read length 15–20 kb 150 bp 10–100 kb
Median read accuracy
99.95% (Q33)1
99.92% (Q31)2
98.90% (Q19)3
Coverage Unbiased Reduced at low and high [GC] Reduced in low-complexity runs
Variant calling: SNVs4
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Variant calling: indels4
Variant calling: SVs4
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Genome assembly: contiguity5,6
Genome assembly: accuracy5,6
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Areas of high homology (pseudogenes, dark regions) __
Phasing

* via raw reads

1. Read accuracy PacBio HiFi: precisionFDA Truth Challenge V2
2. Illumina: HG002 2×150 bp NovaSeq library, precisionFDA Truth Challenge V2
3. ONT: Q20+ chemistry (R10.4, Kit 12), Oct 2021 GM24385 Q20+ Simplex dataset release
4. Shafin Nat Methods 2021 (https://doi.org/10.1038/s41592-021-01299-w)
5. Cheng 2021 Nat Methods (https://doi.org/10.1038/s41592-020-01056-5)
6. Shafin 2020 Nat Biotech (https://doi.org/10.1038/s41587-020-0503-6)

HUMAN GENOME MAPPING TO UNDERSTAND HUMAN HEALTH AND DIVERSITY

PAVE A PATH TO DIAGNOSTIC DISCOVERY

With >99.9% accuracy and long read lengths up to 25 kb, HiFi sequencing allows scientists to find causative pathogenic variants and identify novel disease-associated genes through:

Best-in-class variant calling for all variant types

HiFi sequencing includes solutions for single nucleotide variants (SNV), indels, copy number variants (CNVs), structural variants (SVs) and repeat expansions.

Complete, accurate, and phased assemblies of the human genome

Sequence regions previously inaccessible to other technologies — for accurate typing of genes including HLA and CYP2D6.

Uniform coverage

Achieve the coverage needed to access the complete size spectrum of cancer mutations so that you can:

  • Reveal patterns of structural variants
  • Characterize genotypic differences between cohorts that respond differently to treatment by phasing distant SNPs or identifying structural variants
  • Look beyond SNVs and robustly detect all structural variants to reveal novel insights not possible with short-read sequencing

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Short read sequencing vs. HiFi reads graph - PacBio

IDENTIFY GENETIC DRIVERS OF DISEASE

To identify the genetic drivers of diseases, scientists must have access to the complete genomic landscape, including regions previously deemed impossible to sequence, and the tools to examine the full range of genomic variation.

The PacBio systems using Single Molecule, Real-Time (SMRT) sequencing provide exceptionally long reads, uniform coverage, and high consensus accuracy. This technology enables scientists to gain a more comprehensive understanding of the genetic basis of disease.

UNDERSTAND HOW TO HARNESS THE BENEFITS OF MEDICATION

Pharmacogenomics (PGx) impacts patient care by utilizing genomic information to assess an individual’s response to certain medications. PGx can be used to predict adverse drug reactions or decreased efficacy, leading to improved health outcomes and decreased costs. An estimated 99% of people have actionable variants in PGx genes1,2, and studies have shown that up to 55% of adults2 are prescribed drugs for which there are PGx guidelines available. HiFi sequencing provides high resolution insight into PGx loci, which include complex variants such as pseudogenes, tandem repeats, and CNVs.

1. McInnes G, Lavertu A, Sangkuhl K, Klein TE, Whirl-Carrillo M, Altman RB. Pharmacogenetics at scale: An analysis of the UK Biobank. Clin Pharmacol Ther. 2021 Jun;109(6):1528-1537. doi: 10.1002/cpt.2122. Epub 2020 Dec 17. PMID: 33237584; PMCID: PMC8144239.
2. Chanfreau-Coffinier C, Hull LE, Lynch JA, DuVall SL, Damrauer SM, Cunningham FE, Voight BF, Matheny ME, Oslin DW, Icardi MS, Tuteja S. Projected prevalence of actionable pharmacogenetic variants and level A drugs prescribed among US Veterans Health Administration pharmacy users. JAMA Netw Open. 2019 Jun 5;2(6):e195345. doi: 10.1001/jamanetworkopen.2019.5345. PMID: 31173123; PMCID: PMC6563578.

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Roundel image of microbes on blue background for complexities of immunity

UNCOVER THE COMPLEXITIES OF IMMUNITY

From SNVs to structural variants, isoforms and somatic hypermutation, see the full range of variation that impacts the immune response in infectious disease, cancer, or autoimmunity.

The loci encoding the critical components of the vertebrate immune system are at once highly variable from person to person and hard to sequence. Only HiFi sequencing combines single-molecule accuracy with long read lengths, allowing you to:

  • Generate fully phased haplotypes of immunologically important NGS dead zones including the KIR and IGH loci
  • Determine HLA haplotypes unambiguously and without imputation
  • See the full diversity of the adaptive immune response in action with full- length transcripts and isoforms in targeted, bulk, or single-cell experiments

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FEATURED SEQUENCING SYSTEMS

Our portfolio of sequencers drive improvements in rare disease research, inspire personalized approaches to medicine, and enbale the promise of genomics to better human health.

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