Menu

Human genomics

Uncompromising power to unlock the genome to improve human health

Connect with a PacBio scientist

HUMAN GENOMICS SOLUTIONS

PacBio HiFi sequencing delivers highly accurate, single-molecule long reads for analyzing both DNA and RNA, allowing you to explore the full extent of human genetic variation with a more comprehensive view of the genome, transcriptome, and epigenome than ever before. The benefits of HiFi sequencing — and its numerous applications in human genomics — are ready to enable your next great discovery.

white rare disease icon

RARE DISEASE

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

Learn more

white pgx_pharmacogenomics icon

PHARMACOGENOMICS

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

Learn more

white neurogenomics icon

NEUROGENOMICS

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

Learn more

white hla icon

HLA

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

Learn more

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
__ __
Variant calling: indels4
Variant calling: SVs4
__
Genome assembly: contiguity5,6
Genome assembly: accuracy5,6
__
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)

Brochure

Human genomics overview

The length and accuracy of HiFi reads allow you to access genomic dark regions such as areas of high homology, GC-rich and repetitive regions, and to resolve complex gene families like HLA and pharmacogenes like CYP2D6. PacBio HiFi reads are typically around 15 kb in length with an accuracy of 99.9% and can sequence through GC-rich regions and even repeats in segmental duplications and centromeres — all while delivering simultaneous 5-methylcytosine (5mC) calls for a commanding view of the genome.

Learn more

HUMAN GENOMICS IN ACTION

Complete sequence of a human genome cover image - PacBio

THE COMPLETE SEQUENCE OF A HUMAN GENOME

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

Learn more

PureTarget logo masonry image

Repeat expansion panel for clinical research

The PureTarget repeat expansion panel offers a robust, end-to-end workflow designed to reduce iterative testing using legacy technology and reduce the time needed to identify neurological disease-causing variants and associated methylation signatures.

Learn more

glowing blue brain image

FULL-LENGTH RNA SEQUENCING OF ALZHEIMER’S

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

Learn more

Sprite decoration

EXPLORE

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

Explore resources

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, a 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.

Sprite decoration

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 A MORE 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 HiFi technology was used by the Telomere-to- Telomere (T2T) Consortium to fill in those gaps.

Roundel of Neurons on black background

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

ACHIEVE FEWER ERRORS DURING VARIANT DETECTION

PacBio 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

Roundel image of vials being filled by a pipette for Overcome pgx challenges

Sprite decoration

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.

“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

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.

Read More

APPLICATIONS TO FUEL HUMAN GENOMICS RESEARCH

WHOLE GENOME SEQUENCING

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

Learn more

RNA SEQUENCING

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

Learn more

TARGETED SEQUENCING

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

Learn more

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 probable causative variants.

Learn more

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 possible 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.

More 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 a more 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

Sprite decoration
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 a more complete genomic landscape, including regions previously deemed nearly 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 genes,1,2 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.

Sprite decoration
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

Sprite decoration

FEATURED SEQUENCING SYSTEMS

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

Explore products

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.