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MGL-NICHD provides sequence information, including possible damaging mutations, on potentially disease causing genes of patients diagnosed with one or more disorders by NICHD Principal Investigators. The proposed technology is Next Generation Sequencing (NGS) Solid 4 platform (Applied Biosystems) after targeted enrichment of the genomic regions of interest (Agilent Technologies). The sequence analysis is conducted under CLIA laboratory conditions (CLIA ID# 21D2007566), and the results are reported to the requesting physicians; the testing is covered by protocols/consents held by the requestors. The positive variants of interest are confirmed by bi-directional Sanger sequencing.
For efficiency, on every Solid 4 run, additional genes are analyzed. The sequence information on these additional genes, and Sanger confirmation of the identified variants, will be available to the corresponding PIs under request. In general, sequence information on the additional genes will be made anonymous and will be used for research purposes only.
Individual patients and/or kindreds will be referred for analysis by the NICHD PIs after written request. A total of five-hundred patients are anticipated to be referred for analysis every year. Enrollment protocols and informed consents will be held by the requestor. MGL-NICHD accepts as a specimen type only purified human DNA. DNA specimen is subject of rejection if does not satisfy the MGL-NICHD requirements for quality and quantity.
For more information and forms relating to diagnostic tests, visit the Molecular Genomics Lab site.
Sending a Specimen
To request a test, the referring physician must download and complete Test Requisition Form, and send it with the Specimen. The instructions for Specimen Collection and Handling are provided: Specimen Collection and Handling. All forms are available at the Molecular Genomics Lab site.
Our Protocol (Outlines)
- Targeted DNA enrichment of selected regions of interest
Purified genomic DNA will be used to generate enriched library of the exons and the flanking intronic regions (10 to 30 bp) of the genes of interest. The library will be generated using Sure Select Target enrichment system provided by Agilent Technologies.
- Sequencing of the enriched libraries on Solid 4 platform
The enriched DNA libraries will be sequenced on SOLiD 4 platform. SOLiD 4 platform enables generation of 100GB high-quality sequence data per run, with high accuracy based on dinucleotide-produced signals (as opposed to single-nucleotide-based signals).
- Data Analysis
The resulting sequence datasets are subjected to primary and secondary analysis.
Primary analysis aims to assure proper data production and includes alignment of the sequencing data against short (up to 100 megabases) reference sequence. It is performed by manufacturer provided (Applied Biosystems) software, integrated in the Solid 4 computer system.
Secondary analysis includes fine reading and assembly of all the generated sequencing reads, variation analysis, and analysis of the pathogenic potential of the identified variants. For optimal performance, secondary analysis can be run on several platforms in parallel:
- Bioscope Integrated hardware-software package (Applied Biosystems)
- Bowtie: short read aligner optimized for ultrafast performance on human data.
- Additional analyses software may be use, as needed.
For diagnostic purposes, all the identified variations of interest will be confirmd with by-directional Sanger sequencing.
After completion of the analysis on the PI-requested genes and confirmation of the variations of interest, the sequence results on the inquired genes will be reported to the requesting PI under the CLIA protocol