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Biobank Genomics Core

Next-Generation Sequencing

We offer next-generation sequencing for a range of sequencing read lengths and coverage as well as library construction services.

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Biobank Genomics Core next-generation sequencing 

The Biobank Genomics Core at Mass General Brigham Personalized Medicine has a strong history of producing the highest quality data for collaborators and clients. Our goal is to help investigators advance their basic and translational research programs by providing exceptional service, technical expertise, and leading sequencing technologies.

We offer next-generation sequencing on the Illumina NovaSeq 6000, offering a range of sequencing read lengths and coverage for customer produced libraries, as well as for incoming DNA or RNA for our suite of library construction services.

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Illumina sequencers

The Illumina NovaSeq 6000 Sequencer uses massively parallel sequencing-by-synthesis technology to generate sequence data with unprecedented throughput and accuracy. This powerful sequencer is ideal for sequencing genomes, exomes, transcriptomes, and large targeted panels at higher sequencing coverage.

NovaSeq 6000

Flow Cell Type Estimated PF reads (billion)1 Applications

SP

1.3-1.6

Large whole-genome sequencing, exome and large panel sequencing, transcriptome sequencing, miRNA profiling, Metagenomics and Amplicon-Seq

S1

2.6-3.2

S2

6.6-8.2

S4

16-20

1 Estimated PF (passing filter) reads based on paired end flow cell

Researchers can submit pre-made libraries or purified DNA/RNA for library construction and subsequent sequencing. The Biobank Genomics Core will carry out quality control of all libraries by qPCR prior to sequencing.

Pooling of libraries is available at an additional cost. Pooling information should be added under special service instructions when submitting a Gateway for Integration of Genomic-Proteomic Applications and Data (GIGPAD) batch order into our online LIMS.

Sample Type

Minimum Volume

Solution

Concentration

Fragment Size

Purification

Customer-constructed libraries

20 ul

TE or nuclease free water

20-100 nM (quantiated by picogreen)

Electrophoresis Gel or BioAnalyzer profile should be included

Qiagen QIAquick PCR purification (28104) or Agencourt Ampure XP (A63881) kit

Please submit samples in either VWR free-standing RNase/DNase free 0.5ml tubes (89004-286) or Fisher RNase/DNase free plates (AB-0800). We can provide these tubes/plates free of charge. If samples are submitted in a different container type, there will be a $5 transfer charge per sample.

All incoming DNA and RNA samples submitted will be ensured for quality control (QC) to check concentration and purity by UV-Vis and Picogreen assay using a Qubit Fluorometer. In the case of total RNA, RIN will be analyzed using Agilent Bioanalyzer chips or Tapestation tape. Any sample failing QC will be returned to the customer for replacement. Where no replacement is available, we can process the failing samples but cannot guarantee the success of the library construction, and no attempt to troubleshoot can be made.

Incoming Libraries can be QC’d by Picogreen and qPCR for concentration as well as Tapestation for size estimation.

Prior to delivery of samples or libraries, please place a GIGPAD batch order. For quotes and customer inquiries, please email us.

The Biobank Genomics Core offers several library construction services. We welcome the opportunity to discuss projects with potential clients to ensure the selection of an appropriate method for their scope of work. We also pay attention to changes in researcher focus and technology and welcome discussion with clients and companies for new technology testing and development, collaborative protocol development, and beta-testing of instrumentation and software.

Learn more about our full services from DNA or RNA extraction, plating, and storage.

Library construction is carried out using multiple automation instruments with the ability to process 96 samples per batch allowing consistency and speed to improve turnaround time and accuracy. QC is carried out at several points throughout library construction and sequencing to ensure the production of high-quality sequencing.

Service

Input

Kit

WGS

gDNA

Illumina TruSeq DNA PCR Free

Exome

gDNA

Agilent SureSelect XT with Clinical Research Exome

Whole transcriptome

Total RNA

Illumina Stranded Total RNA Prep with Ribo-Zero Plus

miRNA-Seq

Total RNA

BiooScientific NEXTFLEX Small RNA-Seq v4

Metagenomics

gDNA

BiooScientific NEXTFLEX 16S V4 Amplicon-Seq kit

Custom Amplicon-Seq

gDNA/Amplicon

seqWell plexWell 96

Custom Target enrichment

gDNA

Agilent SureSelect XT with custom capture kit

All DNA samples should be plated into skirted 96-well plates such as AB-0800 from Thermo Fisher. Samples should be normalized to a concentration of 50 ng/ul as quantitated by picogreen in a minimum volume of 20 ul of TE or nuclease free water. DNA should have an OD 260/280 ratio of 1.7-2.0.

All RNA samples should be plated into skirted 96-well plates such as AB-0800 from Thermo Fisher. Samples should be normalized to a concentration of 50 ng/ul as quantitated by OD in a minimum volume of 20 ul of DNase and RNase free water. RNA should have an RNA Integrity Number (RIN) of greater than seven and an OD 260/280 ratio of 1.75-2.0. To avoid freeze thaw of samples to be used for library construction, a QC aliquot containing three ul of RNA is required for each sample submitted. If RNA samples are extracted using Trizol or other organic reagents, the final clean-up step must be performed using a RNeasy column or similar method.

Samples cannot be delivered until an order has been submitted through GIGPAD.

Please contact us 24 hours in advance of delivering any samples to the lab at 65 Landsdowne Street, Suite 350, Cambridge, MA 02139 (Monday-Friday from 9:00 a.m.–12:00 p.m. and 1:00 p.m.–4:00 p.m., closed on holidays).

All samples are subject to QC analysis upon arrival and after processing. Any residual sample material is held in our freezer for 30 days after processing, then are subject to discard without further notice.

We work on a first-come, first served basis. On average, it takes two to three weeks to complete library construction once samples are received. Contact us, see where we are located and submit samples.

Sequencing bioinformatics analysis

The Biobank Genomics Core offers a standard bioinformatics analysis on all libraries sequenced in our facility. This standard analysis package includes the generation and delivery of demultiplexed, unaligned reads in a FASTQ format. In addition, a sample manifest containing library construction and post-alignment quality metrics from our internal QC pipeline will be provided.

Project Type Standard Bioinformatics Service Advanced Services*
Whole Genome (WGS) FASTQ generation
Alignment & coverage QC		 Variant calling
Variant annotations
Variant interpretations
CNV calling
PGX
Whole Exome (WES) FASTQ generation
Alignment & coverage QC		 Variant calling
Variant annotations
Variant interpretations
CNV calling
Targeted Capture FASTQ generation
Alignment & coverage QC		 Variant calling
Variant annotations
Variant interpretations
CNV calling
Amplicon FASTQ generation
Alignment & coverage QC		 Variant calling
Variant annotations
Variant interpretations
RNA FASTQ generation
Alignment QC (including ERCC)		 Differential expression
Gene expression counts
Small RNA FASTQ generation
Alignment QC		 Differential expression
Small RNA counts
Metagenomics FASTQ generation
Alignment QC		 Species-level counts
Genotyping VCF generation
BED/BIM/FAM (if needed)		 Variant annotations
Re-clustering
CNV calling
GWAS

* See Bioinformatics Advanced Services below for more details.

Data delivery options

  • ERISOne DropBox
    • Preferred data delivery method for internal (Mass General Brigham) customers
    • Requires an ERISOne account and a comfort working within a Linux environment
  • Mass General Brigham Transfer Utility
    • Available for external customers and internal customers without ERISOne accounts
    • Limited to 100GB per transfer
  • Encrypted External Hard Drives

Data delivery policy

There is no cost for the initial delivery of project data. Additional charges will apply for the retrieval and delivery of archived data. The estimated turnaround time for the repeated delivery of archived data is one to two weeks.

Bioinformatics advanced services

We offer additional bioinformatics support for both sequencing and biobank projects. Please email us for information on pricing.

Mass General Brigham Personalized Medicine

We offer whole genome and exome sequencing to help detect disease risks and improve the accuracy of diagnoses. Improvements in detection can lead to more targeted, effective, and sometimes preventative care.

Contact us Laboratory for Molecular Medicine Biobank Genomics Core
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