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| Acronym/Term | Definition | Notes | |
|---|---|---|---|
| 10X | Another sequencing company | https://www.10xgenomics.com/ | |
| Adapter | Allows hybridization to the flow cell, contains molecular barcode index (special sequence of synthesized DNA) | ||
| AoU | All of Us | https://allofus.nih.gov/ | |
| Blacklisting | Similar to "flagging" | ||
| bp | Base pair | ||
| BQMS | Broad Quality Management System. Errors & variation tracking. | ||
| BTL | Broad Technology Labs | ||
| Buffy coat | A particular layer of centrifuged blood/cell prep | ||
| CCLF | Cancer Cell Line Factory. Part of the Cancer group at Broad, GP LIMS/Analytics team working with them | ||
| Cell line | |||
| cfDNA | Cell-free DNA | ||
| CI | Continuous Improvement | ||
| CLIA | Clinical | LaboratoryLaboratory Improvement Amendments | https://www.aafp.org/practice-management/regulatory/clia.html |
| CMI | Count Me In. Cancer research project | ||
| CRSP | Clinical Research Sequencing Platform | ||
| ExEx | Exome Express. Special system for faster results turnaround for some exome sequencing products. | ||
| FFP / FFPE | Formaline fixed paraffin embedded (Tissue fixed in formaline and paraffin) | https://www.biochain.com/general/what-is-ffpe-tissue/ | |
| GAP | Genomics Analysis Platform. Obsolete group/LIMS at Broad that has been absorbed into Genomics Platform | ||
| GPLIM | Jira project for GP LIMS | ||
| GSA | Global Screening Array. A chip type | ||
| IDT | A company that synthesizes DNA (e.g. for hybrid selection) | ||
| Infinium | Genotyping platform for Illumina | ||
| Insert size | Length of DNA fragments after shearing, before adapter ligation | ||
| LCSET | Library construction set | ||
| Nexome | Exams processed with kits from Nextera? | ||
| ORSP | Office of Research Subject Protection | ||
| PCR | Polymerase chain reaction | ||
| PDO | Product Order | ||
| Pico | Pico-green, a fluorescent dye used to quant DNA | ||
| Pond, bait, etc. | Hybrid selection terms, hyb sel is a process of creating exomes | ||
| Pooling penalty | How similarly represented the different samples are in a pool of samples | ||
| Qiagen | Company that makes extraction kits | ||
| RGHQS | Regroup H Quality Scores | ||
| RP | Research project | ||
| SNP | Single nucleotide polymorphism | ||
| SPRI | Solid Phase Reversible Immobiization (AMPure by Agencourt) | ||
| TDE | Tableau Data Extract | ||
| TOPMed | Trans-Omics for Precision Medicine | ||
| TSCA | Process used for CCLF samples (among others) | ||
| VBGP | Verily Broad Genomics Platform??? aka "Broad West" | ||
| VVP | Volume verified pipetting. A liquid handler robot from Dynamic Devices | http://dynamicdevices.com/vvp-volume-verified-pipetting/ | |
| WGS | Whole Genome Sequencing |
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