CANDLE Newborn Cord ILMv6.3 (Jun11) QUANT

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The CANDLE Study is a large multidisciplinary study of early child development that involves genetic, genomic, environmental, and large-scale behavioral evaluation of children and their families from the second trimester of development through to 4 years of age. The full study involves more than 1000 children and their mothers and fathers.

For information on genomic and genetic studies related to CANDLE, please contact: Dr. Robert W. Williams ( These data were originally generated by Drs. Ronald M. Adkins and Julia Krushkal at UTHSC.

For information on the composition of neonatal cord blood, please see the review article by Jose N Tolosa and colleagues (2010).

For information on the overall design of CANDLE, please contact: Dr. Frances A. Tylavsky (ftylavsk at

Summary from The Urban Child Institute: "The primary goal of the CANDLE study is to study factors that affect brain development in young children. To this end, the current study will test specific hypotheses regarding factors that may negatively influence cognitive development in children. Participants in this cohort study will include 1,500 mother-child dyads, recruited during the second trimester of pregnancy and followed from birth to age 3. Data on a wide range of possible influences on children's cognitive outcomes will be collected from numerous sources, including questionnaires, interviews, psychosocial assessments, medical chart abstraction, environmental samples from the child's home environment, blood and urine samples from the mother, cord blood, and placental tissue. The primary outcomes of the current study are those associated with a poor cognitive outcome in the child. Outcomes will be measured using standardized cognitive assessments conducted at 12 months, 24 months, and 36 months of age. Epidemiological, clinical, and laboratory-based research may be undertaken using data from the project, with sub-studies including, but not limited to, molecular genetics, environmental exposure assessments, and micronutrient deficiency analyses. Results of this cohort study may provide information that will ultimately lead to improvements in the health, development, and well-being of children in Shelby County, Tennessee through interventions and policy enforcement and/or development. Full participant recruitment and complete data collection began in November 2006."

About cases

A subset of neonatal cord blood samples from the CANDLE cohort.

About tissue

Neonatal cord blood.


Associated References:

  1. Adkins RM, Tylavsky FA, Krushkal J (2012) Newborn umbilical blood DNA methylation and gene expression levels exhibit limited association with birth weight. Chemistry & Biodiversity 9: 888-899
  2. Adkins RM, Thomas F, Tylavsky FA, Krushkal J (2011) Parental ages and levels of DNA methylation in the newborn are correlated. BMC Med Genet 12: 47
  3. Adkins RM, Krushkal J, Tylavsky FA, Thomas F (2011) Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Res A Clin Mol Teratol 91: 728-736



Data Owner: Dr. Robert W. Williams, Dr. Ron Adkins, UTHSC Department of Pediatrics

Expression data generated by the UTHSC Molecular Resources Center with funding from the Center for Integrative and Translational Genomics

Data processing by Drs. Ron Adkins and Julia Krushkal. Data entry into GeneNetwork by Arthur Centeno and Robert W. Williams.

  1. background subtraction (using Illumina's GenomeStudio)
  2. VST transform (using lumi in Bioconductor)
  3. quantile normalization (also using lumi)
  4. [any outliers that did not pass QC were removed using sample clustering, MA plots, boxplots, etc.] correction for batch effects using COMBAT

Please refer to information provided by Drs. Williams or Adkins with the data that specifies exactly which of these steps (or all of them) were included in the final data set that he provided to you.