Blended Genome-Exome Sequencing is now available for clinical applications! Visit our Clinical BGE page.

Human Whole Genome Sequencing

Access both research and clinical-grade whole genome sequencing services backed by 30 years of field-leading experience in providing high quality, reliable data at scale.

Human Whole Genome Sequencing

30x Short read WGS on the
Illumina® NovaSeq X Plus starting at $350

24x Long read WGS on the
PacBio Revio starting at $1600

Services utilizing the
Illumina® NovaSeq X Plus

Services utilizing the PacBio Revio

>650,000 whole genomes sequenced to date

Human Whole Genome Sequencing with Broad Clinical Labs

Short Read WGS Services

Short Read WGS Services

Our WGS services utilize Illumina’s latest technology, the NovaSeq X Plus. All samples for WGS services are processed in our CLIA licensed and CAP accredited facility with rigorous quality control throughout processing. We provide dedicated project management to guide you through project onboarding, sample logistics management, and data delivery.

We offer both PCR-free and PCR-plus Research WGS services. While PCR-free services yield superior coverage evenness and the lowest GC bias, PCR plus services enable high quality data generation from samples whose quality or quantity is limiting (e.g. FFPE).

We offer Clinical WGS services with either a technical report or an interpreted report, depending on your needs.

Long Read WGS Services

Long Read WGS Services

Our long read WGS services utilize PacBio’s latest technology, the Revio™️, to generate HiFi reads using circular consensus sequencing (CCS) sequencing, producing base-level resolution with 99.9% single-molecule read accuracy.

This long read output can be used for de novo sequence assembly, small and large variant detection, haplotype phasing, and epigenetic characterization (methylation).

Compare Human Whole Genome Sequencing Services

ServicesInputsOutputs
PCR-Free WGS on Illumina® Platform (Research); 30x or 60x coverage
  • Whole blood, saliva, buccal swabs, buffy coats, fresh frozen tissue, cell pellets collected in approved devices or;
  • Extracted DNA; ≥1μg total at 10–110 ng/μL concentration; 50–300μL preferred volume, 30 μL minimum acceptable volume
  • CRAM file (aligned to HG38)
  • Single sample VCF
PCR-Plus WGS on Illumina® Platform (Research); 30x or 60x coverage
  • FFPE scrolls, FFPE slides, or genomic DNA (≥300 ng total in 50–300 µL volume; 6–110 ng/µL preferred concentration, 3 ng/µL minimum acceptable concentration) extracted from blood, saliva, buccal swab, buffy coat, fresh frozen tissue, cell pellet, PBMC, or PMN that does not meet the minimum input requirements of the Research PCR-Free product
  • CRAM file (aligned to HG38)
  • Single sample VCF
Long-read WGS on PacBio Platform (Research); 12x or 24x coverage
  • ≥4 µg total mass for single LC attempt (preferred ≥8 µg total) Minimum concentration: 37 ng/µL, Maximum concentration: 110 ng/µL, Minimum volume: 110 µL, Maximum volume: 300 µL
  • For a single LC attempt sample must meet both 37 ng/µL and 110 µL
  • This service is not recommended for samples with any of the following characteristics: Total DNA quantity <4 µg, concentration <30 ng/ul, or volume <100 µL. DNA is significantly degraded (>50% of DNA is smaller than 40kb), WGA or FFPE derived, A260/230 < 1.8OD
  • BAM File
  • FASTQ File
Clinical WGS
(PCR-Free, Illumina® platform)
  • Whole blood in lavender-top (EDTA) tube; saliva, buccal swabs, and buffy coats collected in approved devices; or DNA extracted in a CLIA compliant manner (≥1μg at ≥10 ng/µL). 350 ng of DNA is used for processing, with the remaining material available for rework and QC
  • A test order from an authorized individual
  • Clinical technical-only WGS: CRAM, VCF, and technical report (pdf)
  • Clinical WGS with interpreted report: interpretation report (PDF and/or JSON), delivered through a secure online portal or API with sequencing data (CRAM) available upon request
ServicePCR-Free WGS on Illumina® Platform (Research); 30x or 60x coverage
Inputs
  • Whole blood, saliva, buccal swabs, buffy coats, fresh frozen tissue, cell pellets collected in approved devices or;
  • Extracted DNA; ≥1μg total at 10–110 ng/μL concentration; 50–300μL preferred volume, 30 μL minimum acceptable volume
Outputs
  • CRAM file (aligned to HG38)
  • Single sample VCF
ServicePCR-Plus WGS on Illumina® Platform (Research); 30x or 60x coverage
Inputs
  • FFPE scrolls, FFPE slides, or genomic DNA (≥300 ng total in 50–300 µL volume; 6–110 ng/µL preferred concentration, 3 ng/µL minimum acceptable concentration) extracted from blood, saliva, buccal swab, buffy coat, fresh frozen tissue, cell pellet, PBMC, or PMN that does not meet the minimum input requirements of the Research PCR-Free product
Outputs
  • CRAM file (aligned to HG38)
  • Single sample VCF
ServiceLong-read WGS on PacBio Platform (Research); 12x or 24x coverage
Inputs
  • ≥4 µg total mass for single LC attempt (preferred ≥8 µg total) Minimum concentration: 37 ng/µL, Maximum concentration: 110 ng/µL, Minimum volume: 110 µL, Maximum volume: 300 µL
  • For a single LC attempt sample must meet both 37 ng/µL and 110 µL
  • This service is not recommended for samples with any of the following characteristics: Total DNA quantity <4 µg, concentration <30 ng/ul, or volume <100 µL. DNA is significantly degraded (>50% of DNA is smaller than 40kb), WGA or FFPE derived, A260/230 < 1.8OD
Outputs
  • BAM File
  • FASTQ File
  • Expected output for 12X deliverable is ~37Gb, ≥10kB and for 24X deliverable ~74Gb, ≥10kB
ServiceClinical WGS (PCR-Free, Illumina® platform)
Inputs
  • Whole blood in lavender-top (EDTA) tube; saliva, buccal swabs, and buffy coats collected in approved devices; or DNA extracted in a CLIA compliant manner (≥1μg at ≥10 ng/µL). 350 ng of DNA is used for processing, with the remaining material available for rework and QC
  • A test order from an authorized individual
Outputs
  • Clinical technical-only WGS: CRAM, VCF, and technical report (pdf)
  • Clinical WGS with interpreted report: interpretation report (PDF and/or JSON), delivered through a secure online portal or API with sequencing data (CRAM) available upon request

Applications

Research

Clinical

Medical and population studies

Disease risk screening

Disease research

Carrier screening

Genome-wide association studies

Diagnostics (gene panel or whole genome)

Biomarker discovery

Clinical trials

Gene-edit screening and QC

Pharmacogenomics

Research

Medical and population studies

Disease research

Genome-wide association studies

Biomarker discovery

Gene-edit screening and QC

Clinical

Disease risk screening

Carrier screening

Diagnostics (gene panel or whole genome)

Clinical trials

Pharmacogenomics

Project Workflow- Whole Genome Sequencing

Project onboarding

Project onboarding
(contracting if required)

Regulatory Review
Quoting
Sample Kits

Sample intake and QC
(extraction optional)

Sample types vary by platform and service

Clinical includes: whole blood, buccal swab, saliva

Library Receipt at BCL

Library construction

PCR-Free
PCR-Plus
PacBio CCS

Sequencing

Sequencing

Illumina (short read)
PacBio (long read)

Data delivery

Data and report delivery
(bioinformatic analysis optional)

See table above for available research and clinical service deliverables

Data delivered via secure
Cloud based platform

To get started with Human Whole Genome Sequencing services, please fill out the appropriate form, and a project manager will reach out to you.

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Sean Hofherr

Chief of Clinical Strategy and Product Development, Broad Clinical Labs

Sean Hofherr is dual board certified by ABMGG in Clinical Biochemical Genetics and Clinical Molecular Genetics. Sean serves as the Chief of Clinical Strategy and Product Development at Broad Clinical Labs. In this role at BCL, Sean is able to leverage his extensive experience to guide the clinical vision and delivery across the organization. Sean most recently served as the Chief Operating Office at Fabric Genomics, which focuses on the use of AI and Bioinformatics for Clinical Interpretation of whole genome sequencing. Prior to Fabric, Sean was the Chief Scientific Officer and CLIA Director at the commercial reference laboratory, GeneDx.

Sean received his B.S. degree in Microbiology and Cell Sciences from the University of Florida before earning his Ph.D. in Molecular and Human Genetics from Baylor College of Medicine. Sean completed clinical fellowships in Clinical Biochemical Genetics and Clinical Molecular Genetics at the Mayo Clinic.

Danielle Perrin

Chief of Staff, Broad Clinical Labs

As Broad Clinical Labs’ Chief of Staff, Danielle Perrin advises and supports colleagues on the executive leadership team in BCL’s strategic planning and execution. She builds and leads new organizational functions and processes and leads critical projects, as well as driving effective information flow, decision making, and execution throughout the organization. An operations leader with a business, engineering, and biology background and 20+ years of experience in the genomics field, Perrin has a track record of driving operational excellence and building and scaling both physical and business processes. During her career at Broad, which started in 2003 at the tail end of the Human Genome Project, Perrin has led laboratory operations and R&D teams in Broad’s Genomics Platform, as well as fulfilling senior advisory and leadership roles in the Broad Institute’s COO and CFO offices.

Perrin received her B.S. in Biology and M.E. in Biotechnology Engineering from Tufts University and her M.B.A. from the MIT Sloan School of Management.

Tim De Smet

Chief Commercial Officer, Broad Clinical Labs

As Chief Commercial Officer of Broad Clinical Labs, Tim De Smet leads BCL’s business development, alliance management, external project management, and customer support teams. A Broad Institute employee since 2008, De Smet has held leadership roles and managed teams of various sizes in Broad’s Genomics Platform and clinical lab, spanning laboratory operations, finance, and informatics, and has expertise in work design, financial modeling, and high scale laboratory and business operations.

De Smet received his B.S. in Biochemistry and M.B.A. from Northeastern University.

Jim Meldrim

Chief Technology Officer, Broad Clinical Labs

As Chief Technology Officer, Jim Meldrim sets the vision for Broad Clinical Labs’ informatics systems, including the hardware and software used for sample intake and tracking, data production, analysis, and delivery. Having held a variety of laboratory and informatics-focused leadership roles at Broad, spanning R&D and production operations, Meldrim has been a leader and innovator in the generation, management, and analysis of genomic data since 1999, beginning with sequencing data generation for the Human Genome Project.

Meldrim received his B.S. in Biology from Cornell University.

Sheila Dodge

Chief Operating Officer, Broad Clinical Labs

As Chief Operating Officer, Sheila Dodge leads Broad Clinical Labs’ process development and implementation activities, as well as lab operations, financial planning and operations, quality & compliance, and core business processes. A Six Sigma Black Belt with extensive experience in process development and high throughput genomics operations, Dodge is an expert in work design and in collaborating with a range of collaborators, scientists, engineers, and technology partners to rapidly integrate new technologies and operationalize innovations. A member of the Broad Institute since 2001, Dodge is an Institute Scientist and lectures at the MIT Sloan School of Management on operations, dynamic work design, and visual management techniques.

Dodge received her B.A. in biochemistry and molecular biology from Boston University and her master’s degree in biology from Harvard University. She earned her M.B.A. from MIT Sloan School of Management.

Heidi Rehm, Ph.D., FACMG

Chief Medical Officer and Clinical Laboratory Director, Broad Clinical Labs

Heidi Rehm is board-certified by ABMGG in Clinical Molecular Genetics and Genomics and serves as BCL’s Chief Medical Officer and Clinical Laboratory Director. She oversees BCL’s regulatory requirements, leads the clinical team performing genomic interpretation and variant analysis, and guides BCL’s efforts in genomic testing for clinical and research use. She is also an Institute Member of the Broad and co-director of the Medical and Population Genetics Program. Rehm is also the Chief Genomics Officer in the Department of Medicine and Genomic Medicine Unit Director at the Center for Genomic Medicine at Massachusetts General Hospital, working to integrate genomics into medical practice. She is a principal investigator of ClinGen, providing free and publicly accessible resources to support the interpretation of genes and variants. She co-leads both the Broad Center for Mendelian Genomics, focused on discovering novel rare disease genes, and the Matchmaker Exchange, which aids in gene discovery. She is Chair of the Global Alliance for Genomics and Health, a principal investigator of the Broad-LMM-Color All of Us Genome Center, co-leader of the Genome Aggregation Database (gnomAD), and a Board Member and Vice President of Laboratory Genetics for the American College of Medical Genetics and Genomics.

Rehm received her B.A. degree in molecular biology and biochemistry from Middlebury College before earning her M.S. in biomedical science from Harvard Medical School and Ph.D. in genetics from Harvard University. She completed her post-doctoral training with David Corey in neurobiology and a fellowship in clinical molecular genetics at Harvard Medical School.

Niall Lennon, Ph.D.

Chair and Chief Scientific Officer, Broad Clinical Labs

As Chair and Chief Scientific Officer of Broad Clinical Labs, Niall Lennon leads the team and sets the scientific and clinical vision for the organization. Dr. Lennon joined the Broad Institute in 2006 and has since contributed to the development of applications for every major massively parallel sequencing platform across a range of fields. In 2013 Dr. Lennon led the effort to establish a CLIA licensed, CAP-accredited clinical laboratory at the Broad Institute to facilitate return of results to patients and to support clinical trials. More recently, he has led efforts to achieve FDA approval for large-scale genomics projects (NIH’s All of Us Research Program) and for Broad’s own clinical diagnostic for COVID-19 testing operation, which returned 37+ million results to patients. Dr. Lennon is a principal investigator of the eMerge and All of Us projects, an Institute Scientist at Broad, Associate Director of Broad’s Gerstner Center for Cancer Diagnostics, and an adjunct professor of biomedical engineering at Tufts University, where he teaches Molecular Biotechnology.

Dr. Lennon received a Ph.D. in pharmacology from University College Dublin and completed his postdoctoral studies at Harvard Medical School and Massachusetts General Hospital. He holds an executive certificate in management from the MIT Sloan School of Management.