The Center for Inherited Disease Research (CIDR) provides high-quality next generation sequencing, genotyping, and supporting statistical genetics services to intramural and extramural investigators working to discover genes that contribute to human health and disease. Access to CIDR services is through an expedited peer-review process.

The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA screens, informatics/pathway analysis and rigorous follow-up. Genome-wide siRNA screens for human and mice are available. Also routinely included in screens are miRNA mimic and inhibitor libraries.

NISC\’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to bring genomic sequence to biology and medicine. We accomplish this by meeting with each NIH investigator to discuss the details of their project to determine which method(s) would work best. The most common types of sequencing projects include whole exome sequencing, RNA sequencing, custom capture sequencing, CHiP-seq and whole genome sequencing. However, we are always interested in exploring new methods and expanding our repertoire in this rapidly changing field. We also work closely with other investigators across the NHGRI Intramural Research Program to develop novel methods to analyze genomics data with applicability to clinical and basic science questions that were thought to be intractable only a few years ago.

Contact Details

Director: Jim Mullikin
Phone: (301) 496-2416
Email: mullikin@mail.nih.gov
Address: Room 5S-16 5625 Fishers Lane Rockville, MD 20852 USA

List of Services

Whole Exome Sequencing and Analysis – FAQ
Bulk RNA-Seq – FAQ
Single-Cell RNA-Seq – FAQ
ChIP-Seq – FAQ
Whole genome sequencing (Eukaryotic and microbial) – FAQ
Amplicon sequencing
Custom capture projects – FAQ

Initiating A Project – If you are thinking about initiating a new sequencing project, please visit https://www.nisc.nih.gov/contact.cgi. After this form is submitted, we will set up a meeting with you to plan the best approach for your needs. Please note that our sequencing service is restricted to intramural investigators at the NIH. Human DNA samples will need to be properly consented and de-identified.

Library Construction - NISC has a highly skilled library construction group able to make a wide range of libraries compatible with all of our sequencing platforms. You deliver high-quality DNA or RNA and we construct the library. We prefer to start a sequencing project at this point, which allows our experienced hands to control each step for optimal performance and ensure the highest rate of success at the end.

Data Return – The raw data from the sequencers is extensively processed, and data is evaluated for quality. For Illumina data, the general deliverable is fastq files which contain the base calls as well as sequence quality scores.

Exome Analysis - NISC provides data analysis for all human whole exome and custom capture sequencing projects. Variants, genotypes, and annotations are delivered to the investigator in tab-delimited format compatible with VarSifter, a java-based genotype viewer, available from NISC. We hope to provide this analysis for human whole genome sequencing projects in the near future.

Established Technologies

Illumina NovaSeq 6000
The NovaSeq 6000 offers scalable sequencing through multiple flow cell modules. The most cost-effective module is the S4 which produces ~2.5 Tb per flow cell or ~ 625 Gb per lane. Due to the extremely high quantity of sequence output, this technology is primarily useful for projects requiring a very large number of reads, such as whole genome, whole exome and multiplexed transcriptome experiments. 

Illumina NextSeq 550
The NextSeq 550 is a mid-range output sequencer. Multiple run options are offered, with outputs ranging from 16 Gb to 120 Gb and read lengths from 1 × 75 b to 2 × 150 b. This platform is ideal for smaller projects or those requiring non-standard run conditions, such as single-cell RNA-Seq. 

Illumina MiSeq
MiSeq is a small-scale benchtop sequencer. This instrument is compatible with any of the Illumina libraries described above. MiSeq produces reads up to 300 bases in length from a paired-end read run (2×300 b) with a yield of ~10 Gb. This capability is primarily useful for sequencing microbial genomes and amplicons. 

PacBio Sequel II
The PacBio Sequel II platform generates long read lengths while maintaining high consensus accuracy and unbiased coverage. The maximum read length is more than 50 kb and high fidelity (HiFi) reads >10 kb with >99.9% accuracy can also be generated. This platform can generate sequence reads that support high-quality assemblies from small bacterial genomes all the way up to diploid human genomes. Other applications include amplicons, full length 16s sequencing, epigenomes, and RNA isoforms. For most applications one SMRT cell generates 20-50 Gb of data and completes in 20-30 hours. 

Oxford Nanopore GridION and PromethION
The Oxford Nanopore platform is the newest and most rapidly evolving platform in our portfolio of sequencing technologies. Monitoring current fluctuations as native DNA or RNA molecules pass through nanopores, this approach has key advantages of being able to read ultra-long fragments (some > 1Mb) and detecting modified bases without special library construction. Base calling is done in real time making sequence data available right from the start of the run. Raw read accuracy is currently about 98% with new advances expected to push that over 99%. The primary uses of this technology to date at NISC have taken advantage of the ultra-long reads to detect large structural variants and create de novo genome assemblies. Using this approach, a typical PromethION flowcells yields 80 Gbase of quality reads with N50 approximately 72kb. Preliminary experiments have also been undertaken to explore direct RNA and full-length cDNA sequencing.

 

User Guidelines

The NIH Intramural Sequencing Center provides cost-recovery sequencing services to the NIH Intramural Community.