Clinical Reporting Standard Sequences
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Transcript of Clinical Reporting Standard Sequences
Clinical Reporting Standard Sequences Deanna M. Church Staff Scientist, NCBI
@deannachurch Short Course in Medical Genetics 2013
AcknowledgementsGeT-RM
Lisa Kalman (CDC)Birgit Funke (Harvard)Mahduri Hegde (Emory)Maryam HalaviChao ChenJon TrowDouglas SlottaPeter MericDaniel FrishbergVictor AnanievWendy Rubinstein
GVMSPaul KittsGreg SchulerDonna MaglottLon PhanKim PruittMartin Shumway
Browser/Track Management Victor AnanievCliff Clausen Ark DoubintchikVictor JoukovAnatoliy KuznetsovPeter MericLiangshou WuEugene Yaschenko
Adapted from http://www.ndsu.edu/pubweb/~mcclean/plsc431/homework/positional-cloning/
1990
2000
2010
APCAniridiaFragile X
Myotonic DystrophyNorrie Disease
Huntington DiseaseMenkes Disease
NF2Tuberous Sclerosis
AchondroplasiaBRCA1PKD1
Ataxia TelangiectasiaBloom syndrome
SMA
HemochromatosisLong QT
PKD2Treacher Collins
Alagille SyndromeAngelmanDeafness 1
WolframRetinis Pigmentosa
Deafness 5
http://www.ncbi.nlm.nih.gov/gtr
http://www.ncbi.nlm.nih.gov/refseq/rsg/
http://www.lrg-sequence.org/
SLX4: NG_028123
Many RefSeqGene/LRG sequences are identical to the reference assembly
PKD1: NG_008617
Insertion in PKD1 RefSeqGene
A>GT>Cinsertion
Variants unique to RefSeqGene
Take home messages
Gene testing began before there was a reference assemblySequence as still stable and traceable.Often used in clinical reporting