TY - JOUR
T1 - Twins, tissue, and time
T2 - An assessment of SNPs and CNVs
AU - Scheet, Paul
AU - Ehli, Erik A.
AU - Xiao, Xiangjun
AU - van Beijsterveldt, Catharina E. M.
AU - Abdellaoui, Abdel
AU - Althoff, Robert R.
AU - Hottenga, Jouke Jan
AU - Willemsen, Gonneke
AU - Nelson, Kelly A.
AU - Huizenga, Patricia E.
AU - Hu, Yueshan
AU - Amos, Christopher I.
AU - Bartels, Meike
AU - Groen-Blokhuis, Maria M.
AU - de Geus, Eco J. C.
AU - Hudziak, James J.
AU - Davies, Gareth E.
AU - Boomsma, Dorret I.
PY - 2012/12
Y1 - 2012/12
N2 - With the desire to assess genetic variation across the lifespan in large-scale collaborative projects, one question is whether inference of copy number (CN) is sensitive to the source of material for deoxyribonucleic acid (DNA) analysis (e.g., blood and buccal) and another question is whether CN is stable as individuals age. Here, we address these questions by applying Affymetrix 6.0 single nucleotide polymorphism (SNP) micro-arrays to 1,472 DNA samples from 710 individuals from the Netherlands Twin Register, including twin and non-twin individuals (372 with buccal and blood derived DNA and 388 with longitudinal data). Similar concordance for CN and genotype inference between samples from the same individual [or from the monozygotic (MZ) co-twins] was found for blood and buccal tissues. There was a small but statistically significant decrease in across-tissue concordance compared with concordance of samples from the same tissue type. No temporal effect was seen on CN variation from the 388 individuals sampled at two time points ranging from 1 to 12 years apart. The majority of our individuals were sampled at age younger than 20 years. Genotype concordance was very high (R 2 > 99%) between co-twins from 43 MZ pairs. For 75 dizygotic (DZ) pairs, R 2 was ≈65%. CN estimates were highly consistent between co-twins from MZ pairs for both deletions (R 2 ≈ 90%) and duplications (R 2 ≈ 86%). For DZ, these were similar for within-individual comparisons, but naturally lower between co-twins (R 2 ≈ 50-60%). These results suggest that DNA from buccal samples perform as well as DNA from blood samples on the current generation of micro-array technologies. © The Authors 2012.
AB - With the desire to assess genetic variation across the lifespan in large-scale collaborative projects, one question is whether inference of copy number (CN) is sensitive to the source of material for deoxyribonucleic acid (DNA) analysis (e.g., blood and buccal) and another question is whether CN is stable as individuals age. Here, we address these questions by applying Affymetrix 6.0 single nucleotide polymorphism (SNP) micro-arrays to 1,472 DNA samples from 710 individuals from the Netherlands Twin Register, including twin and non-twin individuals (372 with buccal and blood derived DNA and 388 with longitudinal data). Similar concordance for CN and genotype inference between samples from the same individual [or from the monozygotic (MZ) co-twins] was found for blood and buccal tissues. There was a small but statistically significant decrease in across-tissue concordance compared with concordance of samples from the same tissue type. No temporal effect was seen on CN variation from the 388 individuals sampled at two time points ranging from 1 to 12 years apart. The majority of our individuals were sampled at age younger than 20 years. Genotype concordance was very high (R 2 > 99%) between co-twins from 43 MZ pairs. For 75 dizygotic (DZ) pairs, R 2 was ≈65%. CN estimates were highly consistent between co-twins from MZ pairs for both deletions (R 2 ≈ 90%) and duplications (R 2 ≈ 86%). For DZ, these were similar for within-individual comparisons, but naturally lower between co-twins (R 2 ≈ 50-60%). These results suggest that DNA from buccal samples perform as well as DNA from blood samples on the current generation of micro-array technologies. © The Authors 2012.
KW - Adolescent
KW - Adult
KW - Child
KW - Child, Preschool
KW - DNA Copy Number Variations
KW - DNA/chemistry
KW - Female
KW - Genotype
KW - Humans
KW - Male
KW - Middle Aged
KW - Oligonucleotide Array Sequence Analysis/methods
KW - Polymorphism, Single Nucleotide
KW - Specimen Handling/methods
KW - Twins, Monozygotic/genetics
UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84873855131&origin=inward
UR - https://www.ncbi.nlm.nih.gov/pubmed/23021707
U2 - https://doi.org/10.1017/thg.2012.61
DO - https://doi.org/10.1017/thg.2012.61
M3 - Article
C2 - 23021707
SN - 1832-4274
VL - 15
SP - 737
EP - 745
JO - Twin research and human genetics
JF - Twin research and human genetics
IS - 6
ER -