PMID- 17661425
OWN - NLM
STAT- MEDLINE
DCOM- 20080128
LR  - 20220316
IS  - 1098-1004 (Electronic)
IS  - 1059-7794 (Linking)
VI  - 28
IP  - 12
DP  - 2007 Dec
TI  - Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, 
      and parent of origin effects in single nucleotide polymorphism trio data with 
      SNPtrio.
PG  - 1225-35
AB  - A variety of alterations occur in chromosomal DNA, many of which can be detected 
      using high density single nucleotide polymorphism (SNP) microarrays. These 
      include deletions and duplications (assessed by observing changes in copy number) 
      and regions of homozygosity. The analysis of SNP data from trios can provide an 
      additional category of information about the nature and origin of inheritance 
      patterns, including uniparental disomy (UPD), loss of transmitted allele (LTA), 
      and nonparental relationship. The main purpose of SNPtrio is to locate regions of 
      uniparental inheritance (UPI) and Mendelian inconsistency (MI), identify the type 
      (paternal vs. maternal, iso- vs. hetero-), and assess the associated statistical 
      probability of occurrence by chance. SNPtrio's schema permits the identification 
      of hemizygous or homozygous deletions as well as UPD. We validated the 
      performance of SNPtrio on three platforms (Affymetrix 10 K and 100 K arrays and 
      Illumina 550 K arrays) using SNP data obtained from DNA samples of patients known 
      to have UPD and diagnosed with Prader-Willi syndrome, Angelman syndrome, 
      Beckwith-Wiedemann syndrome, pseudohypoparathyroidism, and a complex chromosome 2 
      abnormality. We further validated SNPtrio using DNA from patients previously 
      shown to have microdeletions that were verified by fluorescence in situ 
      hybridization (FISH). SNPtrio successfully identified previously known UPD and 
      deletion regions, and generated associated probability values. SNPtrio analysis 
      of trisomy 21 (Down syndrome) cases and their parents permitted identification of 
      the parent of origin of the extra chromosomal copy. SNPtrio is freely accessible 
      at http://pevsnerlab.kennedykrieger.org/SNPtrio.htm (Last accessed: 20 June 
      2007).
CI  - (c) 2007 Wiley-Liss, Inc.
FAU - Ting, Jason C
AU  - Ting JC
AD  - Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, 
      USA.
FAU - Roberson, Elisha D O
AU  - Roberson ED
FAU - Miller, Nathaniel D
AU  - Miller ND
FAU - Lysholm-Bernacchi, Alana
AU  - Lysholm-Bernacchi A
FAU - Stephan, Dietrich A
AU  - Stephan DA
FAU - Capone, George T
AU  - Capone GT
FAU - Ruczinski, Ingo
AU  - Ruczinski I
FAU - Thomas, George H
AU  - Thomas GH
FAU - Pevsner, Jonathan
AU  - Pevsner J
LA  - eng
GR  - HD24061/HD/NICHD NIH HHS/United States
GR  - R01HD046598/HD/NICHD NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Hum Mutat
JT  - Human mutation
JID - 9215429
SB  - IM
MH  - Angelman Syndrome/genetics
MH  - Beckwith-Wiedemann Syndrome/genetics
MH  - *Chromosome Deletion
MH  - Female
MH  - Genotype
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - Male
MH  - Nuclear Family
MH  - Polymorphism, Single Nucleotide/*genetics
MH  - Prader-Willi Syndrome/genetics
MH  - Pseudohypoparathyroidism/genetics
MH  - *Software
MH  - Uniparental Disomy/*genetics
EDAT- 2007/07/31 09:00
MHDA- 2008/01/29 09:00
CRDT- 2007/07/31 09:00
PHST- 2007/07/31 09:00 [pubmed]
PHST- 2008/01/29 09:00 [medline]
PHST- 2007/07/31 09:00 [entrez]
AID - 10.1002/humu.20583 [doi]
PST - ppublish
SO  - Hum Mutat. 2007 Dec;28(12):1225-35. doi: 10.1002/humu.20583.