Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study

Shona M Kerr; Archie Campbell; Lee Murphy; Caroline Hayward; Cathy Jackson; Louise V Wain; Martin D Tobin; Anna Dominiczak; Andrew Morris; Blair H Smith; David J Porteous

doi:10.1186/1471-2350-14-38

Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study

Shona M Kerr, Archie Campbell, Lee Murphy, Caroline Hayward, Cathy Jackson, Louise V Wain, Martin D Tobin, Anna Dominiczak, Andrew Morris, Blair H Smith, David J Porteous

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity.

Original language	English
Article number	38
Number of pages	7
Journal	BMC Medical Genetics
Volume	14
Issue number	1
DOIs	https://doi.org/10.1186/1471-2350-14-38
Publication status	Published - 22 Mar 2013

Keywords / Materials (for Non-textual outputs)

Pedigree
Family Characteristics
Polymorphism, Single Nucleotide
Humans
Aged
Child
Sequence Analysis, DNA
Research Design
Genotype
Scotland
Adult
Cohort Studies
DNA
Family
Middle Aged
Sample Size
Parents
Family Health
Female
Male

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10.1186/1471-2350-14-38

Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland
© 2013 Kerr et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 389 KBLicence: Creative Commons: Attribution (CC-BY)

http://www.biomedcentral.com/1471-2350/14/38

Cite this

@article{179103b1016a4df089201d62bdb948c4,

title = "Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study",

abstract = "Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity.",

keywords = "Pedigree, Family Characteristics, Polymorphism, Single Nucleotide, Humans, Aged, Child, Sequence Analysis, DNA, Research Design, Genotype, Scotland, Adult, Cohort Studies, DNA, Family, Middle Aged, Sample Size, Parents, Family Health, Female, Male",

author = "Kerr, {Shona M} and Archie Campbell and Lee Murphy and Caroline Hayward and Cathy Jackson and Wain, {Louise V} and Tobin, {Martin D} and Anna Dominiczak and Andrew Morris and Smith, {Blair H} and Porteous, {David J}",

note = "The research corresponds to Project Reference Number GS10056 through the Generation Scotland Management, Access and Publications Policy. GS:SFHS is funded by the Scottish Executive Health Department, Chief Scientist Office, grant number CZD/16/6. Funding: Medical Research Council [MC_PC_U127561128, G0902313] Chief Scientist Office [CZD/16/6/2, CZD/16/6/4] ",

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month = mar,

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doi = "10.1186/1471-2350-14-38",

language = "English",

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journal = "BMC Medical Genetics",

publisher = "BioMed Central",

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TY - JOUR

T1 - Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland

T2 - Scottish Family Health Study

AU - Kerr, Shona M

AU - Campbell, Archie

AU - Murphy, Lee

AU - Hayward, Caroline

AU - Jackson, Cathy

AU - Wain, Louise V

AU - Tobin, Martin D

AU - Dominiczak, Anna

AU - Morris, Andrew

AU - Smith, Blair H

AU - Porteous, David J

N1 - The research corresponds to Project Reference Number GS10056 through the Generation Scotland Management, Access and Publications Policy. GS:SFHS is funded by the Scottish Executive Health Department, Chief Scientist Office, grant number CZD/16/6. Funding: Medical Research Council [MC_PC_U127561128, G0902313] Chief Scientist Office [CZD/16/6/2, CZD/16/6/4]

PY - 2013/3/22

Y1 - 2013/3/22

N2 - Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity.

AB - Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity.

KW - Pedigree

KW - Family Characteristics

KW - Polymorphism, Single Nucleotide

KW - Humans

KW - Aged

KW - Child

KW - Sequence Analysis, DNA

KW - Research Design

KW - Genotype

KW - Scotland

KW - Adult

KW - Cohort Studies

KW - DNA

KW - Family

KW - Middle Aged

KW - Sample Size

KW - Parents

KW - Family Health

KW - Female

KW - Male

U2 - 10.1186/1471-2350-14-38

DO - 10.1186/1471-2350-14-38

M3 - Article

C2 - 23521772

VL - 14

JO - BMC Medical Genetics

JF - BMC Medical Genetics

IS - 1

M1 - 38

ER -

Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study

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Keywords / Materials (for Non-textual outputs)

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