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