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RNA Sequencing

Gain a more holistic view of the transcriptome with Broad Clinical Labs’ RNA Sequencing services. We offer Whole Transcriptome (mRNA) sequencing, Total RNA sequencing, and Transcriptome Capture.

Whole Transcriptome Sequencing

Working closely with scientists within and outside of the Broad Institute, we have performed a thorough evaluation of available technologies and processing conditions inducing read depth, fragment insert size, and sample cleanup to provide the highest quality whole transcriptome sequencing product.

Leveraging core competencies in process design, molecular biology, laboratory automation and integrated LIMS and analysis tools, we are able to process >500 whole transcriptome samples per week (>25,000 annually), and have performed more than 80,000 whole transcriptomes to date.

Expected performance of Broad Clinical Labs’ Whole Transcriptome Sequencing service
Expected performance of Broad Clinical Labs’ Whole Transcriptome Sequencing service
Typical gene body coverage percentile
(relative coverage) 5’ to 3’ across the transcript
Typical gene body coverage percentile (relative coverage) 5’ to 3’ across the transcript
Comparison of the number of transcripts detected in 20 blood samples processed with both mRNA and Total RNA workflows.

Comparison of the number of transcripts detected in 20 blood samples processed with both mRNA and Total RNA workflows.

Total RNA Sequencing

High complexity cDNA libraries, depleted of globin and rRNA, enable high sequencing depth of up to 100 million reads aligned in pairs and the identification of coding and non coding regions with roles in regulatory mechanisms, as well as detection of alternative splicing events and post-translational modifications that provide a deeper understanding of gene regulation and isoform diversity.

Transcriptome Capture

Transcriptome capture is an alternative to traditional transcript enrichment methods, including poly(A) selection and ribosomal depletion, and is optimal for low-input and degraded samples including RNA from formalin-fixed paraffin-embedded (FFPE) tissues.

Hybridization of libraries to specialized probes enriches for mRNA transcript fragments covering the complete mitochondrial genome and ACMG59 genes, as well as RefSeq and Online Mendelian Inheritance in Man (OMIM) putative gene sequences, Catalog of Somatic Mutations in Cancer (COSMIC) variants, key promoters, and other motifs that have been identified as potential cancer hot spots.

Input Requirements

S1

S2

S3

S4

S5

S6

Median
CV Cov.

1.09

1.16

1.02

0.959

1.11

1.29

% Correct
Strand Reads

98.5

98.0

98.4

97.6

97.6

96.1

% mRNA

84.1

82.4

86.0

85.7

88.0

87.6

% PF Reads Aligned

99.3

94.6

97.4

98.6

98.4

98.8

% Dup.

38.3

50.8

39.1

59.9

58.1

54.8

Representative analytical (hg19) and quality metrics generated using FFPE derived RNA

Sample

S1

S2

S3

S4

S5

S6

Median
CV Cov.

1.09

1.16

1.02

0.959

1.11

1.29

% Correct
Strand Reads

98.5

98.0

98.4

97.6

97.6

96.1

% mRNA

84.1

82.4

86.0

85.7

88.0

87.6

% PF Reads Aligned

99.3

94.6

97.4

98.6

98.4

98.8

% Dup.

38.3

50.8

39.1

59.9

58.1

54.8

Representative analytical (hg19) and quality metrics generated using FFPE derived RNA

Compare RNA Sequencing Services

ServicesWhole Transcriptome Sequencing: 50 million or 100 millon reads aligned in pairs
Inputs
Minimum Volume/Concentration≥250 ng purified total RNA
Sample typesPurified total RNA; or fresh/frozen tissue, blood or cell pellets that yield ≥250 ng purified total RNA
OutputsDemultiplexed, aggregated, aligned BAM file
ServicesTotal RNA Sequencing: 80-100 million reads aligned in pairs
Inputs
Minimum Volume/Concentration≥2 µg purified total RNA (≥50 µL, ≥40 ng/µL)
Sample typesPurified total RNA derived from blood
OutputsDemultiplexed, aggregated, aligned CRAM file
ServicesTranscriptome Capture: 50 million reads aligned in pairs
Inputs
Minimum Volume/Concentration≥550 ng purified total RNA (≥12 ng/µL); ≥1 µg preferred
Sample typesPurified total RNA that is FFPE derived or low quality; other sample types available for processing (blood, stool, cell pellets)
OutputsDemultiplexed, aggregated, aligned BAM file
Services
Inputs
Minimum
Volume/Concentration
Sample types
Outputs
Whole Transcriptome Sequencing: 50 million or 100 million reads aligned in pairs≥250 ng purified total RNAPurified total RNA; or fresh/frozen tissue, blood or cell pellets that yield ≥250 ng purified total RNADemultiplexed, aggregated, aligned BAM file
Total RNA Sequencing: 80-100 million reads aligned in pairs≥2 µg purified total RNA (≥50 µL, ≥40 ng/µL)Purified total RNA derived from bloodDemultiplexed, aggregated, aligned CRAM file
Transcriptome Capture: 50 million reads aligned in pairs≥550 ng purified total RNA (≥12 ng/µL); ≥1 µg preferredPurified total RNA that is FFPE derived or low quality; other sample types available for processing (blood, stool, cell pellets)Demultiplexed, aggregated, aligned BAM file

Services

Whole Transcriptome Sequencing:
50 million or 100 million reads aligned in pairs

Total RNA Sequencing: 80-100 million reads aligned in pairs

Transcriptome Capture:
50 million reads aligned in pairs

Inputs

Minimum
Volume/Concentration

Sample types

≥250ng purified total RNA

Purified total RNA; or fresh/frozen tissue, blood or cell pellets that yield ≥250 ng purified RNA

≥2µg total (≥50 µL, ≥40 ng/µL)

Purified total RNA derived from blood

≥550 ng (≥12 ng/µL concentration) of purified total RNA; ≥1 µL prefered

FFPE or low quality RNA; other sample types available for processing (blood, stool, cell pellets)

Outputs

Demultiplexed, aggregated, aligned BAM file

Demultiplexed, aggregated, aligned CRAM file

Demultiplexed, aggregated, aligned BAM file

Project Workflow

Project onboarding

Project onboarding
(contracting if required)

Regulatory Review
Quoting
Sample Kits

Sample intake and QC

Sample intake and QC
(extraction optional)

Sample QC (including fingerprinting if DNA match sent)

Sample input requirements vary by RNA sequencing service

ERCC RNA control addition (Whole transcriptome)

Library Receipt at BCL

Library construction

Specialized protocol for each RNA sequencing service

Sequencing

Sequencing

Illumina NovaSeq X
Illumina NovaSeq SP

Data delivery

Data and report delivery
(bioinformatic analysis optional)

Data delivered via secure cloud platform

See table above for data deliverables

To get started with RNA Sequencing services, please complete the form below, 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.