MGB PM Biobank Genomics Core

 

At Your Service


At Mass General Brigham Personalized Medicine Biobank Genomics Core, our comprehensive technical expertise, high quality sample handling workflow, leading genomics technologies, and high-quality service has helped genetics investigators advance their genomic research programs for more than a decade. Our goal is to make these technologies accessible for all research projects, small and large, while offering the best customer service in the industry.  The Core welcomes 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. 


Sample Handling services

We offer a range of DNA extraction services for Fresh whole blood drawn in purple top K2 EDTA or K3 EDTA tubes, Saliva collected in Oragene OGR-500.  We also offer total RNA and miRNA extraction services from PaxGene tubes.  Extraction services include quality control of the extracted sample by Picogreen (DNA) and Optical Density, and determination of quality of the extraction using RNA Integrity Number (RIN) for RNA.  DNA and RNA plating is carried out using workflows driven by our LIMs to direct our Automated liquid handling systems to accurately plate DNA or RNA onto 96-well plates.  Samples can be normalized to requested concentrations during this process.   Incorporation of control DNA or RNA samples, such as NA12878 DNA or Universal Human Control RNA can also be requested.

Sample Storage and retrieval services are available to users performing downstream processing within the MGB Biobank Genomics Core.  Currently our storage system allows the storage of PaxGene blood tubes, DNA, RNA, Plasma, Serum and Buffy coat.

On arrival, all samples are accessioned into our LIMs, and Freezer locations are tracked using unique barcodes.  DNA and RNA extractions result in the creation of master tubes and daughter tubes to allow storage of specimens from a subject to be stored within multiple freezers to ensure safe storage of the sample in case of any freezer issue.  All freezers are monitored 24/7 using a remote alarm system and staff are on call 24 hours a day to resolve any issue.  Samples are stored as part of a study allowing only access to those samples by PI approved researchers.  Storage is charged per vial, tube or plate on a monthly basis.

Next-Gen Library Construction and Sequencing using Illumina Novaseq 6000 platform 

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

Current Library Construction Services

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 v3

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


Next-Gen Sequencer

The Biobank Genomics Core at Mass General Brigham Personalized Medicine features an Illumina NovaSeq 6000. This instrument uses massively parallel sequencing-by-synthesis technology to generate sequence data with unprecedented throughput and accuracy. This sequencer is ideal for sequencing genomes, exomes, transcriptomes, and large targeted panels at higher sequencing coverage.  

Sequencer

Flow Cell Type

Estimated PF reads (billion)1

Applications


Illumina NovaSeq 6000

SP

1.3-1.6


Large Whole-Genome sequencing, Exome and large panel sequencing, Transcriptome Sequencing

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


Next-Gen Sequencing Bioinformatics support 

The Mass General Brigham 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


Viral (COVID)
  • FASTQ generation
  • Alignment & coverage QC
  • Viral detection
  • COVID lineage
  • Variant calling
  • Consensus sequence

Genotyping
  • VCF generation
  • BED/BIM/FAM (if needed)
  • Variant annotations
  • Re-clustering
  • CNV calling
  • GWAS


High-throughput Illumina Genotyping for GWAS and EWAS, Lower-throughput Taqman SNP Genotyping 

The Biobank Genomics Core at MGB Personalized Medicine provides flexible, high-quality, high-throughput SNP genotyping to the MGB research community. We offer genome-wide methylation and genotyping assays on our Illumina iSCAN platform, as well as individual SNP assays using the Taqman Assays from Life Technologies. 


For Illumina Infinium, we stock the Global Diversity Array (GDA), Global Screening Array (GSA) and the Human and Mouse Methylation EPIC array.  We can run any of the commercial arrays available from Illumina, with the exception of Infinium XT products.  Please order reagents and arrays directly from Illumina and have the reagents shipped directly to our lab.  New chip types may require additional processing time for clustering and allele calling on completion of wet lab work, please ask if TAT will be impacted.


Technology

SNP Info

DNA

Concentration

Container

Quantitation

Minimum Volume

Illumina Infinium Genotyping

Fixed Panels

Genomic DNA Only

50 ng/ul

Full-skirted 96-well plate, with well H12 empty for in-house control

Picogreen

20 ul

Taqman

RS# or customer provided sequence information

Genomic or WGA DNA

5-10 ng/ul

Full-skirted 96-well plate, with well H12 empty for in-house control

Picogreen

30 ul

Illumina Infinium Methylation

Human/Mouse

Genomic DNA or Bisulfite-Converted DNA

50 ng/ul of Genomic DNA

Full-skirted 96-well plate, with well H12 empty for in-house control

Picogreen

40 ul


Accounts and Ordering

All of our projects are managed via our customer portal, called Gateway for Integration of Genomic-Proteomic Applications and Data (GIGPAD).

Quotes

For Illumina Next-Gen Sequencing and Genotyping quotes and customer inquiries, please email PPMCore@partners.org

For DNA/RNA Extraction and sample handling service quotes and customer inquiries, please email PPMCENTRALBIOBANK@partners.org


Submit a batch order

Please submit a batch order prior to submitting samples. To do this, you must first set up a GIGPAD account. You also must have a valid MGB IRB # and PeopleSoft number.  To request a login to GIGPAD: Visit http://researchgigpad.partners.org/  and Select “click here to request a login.”


How can I submit samples?

After creation of a GIGPAD batch order please contact us to coordinate delivery of your samples. We generally receive samples Monday through Friday 9am-12pm and 1pm-4pm.  Please bring all GIGPAD batch paperwork with you. 


Where is MGB Personalized Medicine Biobank Genomics Core located?

MGB Personalized Medicine
65 Landsdowne St., 3rd floor
Cambridge, MA 02139-4232
Directions


How do I receive my data?

You will be contacted when data is available. Depending on size, data will be available to view through GIGPAD, be available for download, or can be shipped to you on an external hard drive. Data will remain available from MGB Personalized Medicine for 3 months.


Contact MGB PM Biobank Genomics Core

For Illumina Next-Gen Sequencing and Genotyping quotes and customer inquiries, please email PPMCore@partners.org

For DNA/RNA Extraction and sample handling service quotes and customer inquiries, please email PPMCENTRALBIOBANK@partners.org