Sequenom system

All shared SNVs of the two affected individuals were verified for all members acquired from family A to detect co-segregation, by direct polymerase chain reaction (PCR) amplification followed by Sanger sequencing (PCR primers are listed in Table 3, Invitrogen). The sequencing reactions were conducted on an ABI 3730XL DNA Analyzer.
Genotyping was conducted by the MassARRAY (MALDI-TOF MS) method using the SEQUENOM System (Sequenom, Inc.) to screen the candidate genes in an additional 401 HC individuals (278 sporadic CD patients and 123 UC cases), and the data were analyzed using TYPER 4.0 software. The primer sequences for genotyping were designed and synthesized using Primer 5.0 software (PCR primer sequences are listed in Table 4, and the primers were synthesized by Invitrogen). To further study the genes (DLG1 and PDCL) that we identified through the series of steps listed above, we applied PCR amplification followed by Sanger sequencing to examine all of the exons of DLG1 and PDCL in 25 young and intractable CD cases (the PCR primer sequences are listed in Table 5).
SPSS17.0 statistical software was used for statistical analysis, the measurement data were expressed as means +/− standard deviation (SD). PLINK was performed on analysis of genotype data. P values<0.05 were considered as significant.

938 European-American UM-PCGP early-onset PCa cases were initially genotyped at Wake Forest University using Illumina's HumanHap 660W-Quad v1.1 BeadChip. CGEMS Breast cancer controls were genotyped previously using Illumina's HumanHap550v1 [23] (link). The iControlsDB subjects were genotyped previously using Illumina's HumanHap550v1 (n = 1478) or HumanHap550v3 (n = 1507) commercial genotyping platforms. Follow-up genotyping on JHU subjects was performed at Wake Forest University using the Sequenom system. All the procedures followed the manufacturer's iPLEX Application Guide (Sequenom, Inc. SanDiego, CA) and all the assay reagents were purchased from Sequenom. To ensure the quality of the genotyping, around 2% of the sample duplicates and 2% of the negative controls, in which water was substituted for DNAs, were applied.