Development of a diagnostic DNA chip to screen for 30 autosomal recessive disorders in the Hutterite population.

BACKGROUND: The Hutterites are a religious isolate living in colonies across the North American prairies. This population originated from approximately 90 founders, resulting in a number of genetic diseases that are overrepresented, underrepresented, or unique. The founder effect in this population increases the likelihood that Hutterite couples carry the same recessive mutations. We have designed a diagnostic chip on a fee-for-service basis with Asper Biotech to provide Hutterites with the option of comprehensive carrier screening. METHODS: A total of 32 disease-causing mutations in 30 genes were selected and primers were designed for array primer extension-based testing. Selected mutations were limited to those leading to autosomal recessive disorders, maintaining its primary use as a test for determining carrier status. RESULTS: The DNA chip was developed and validated using 59 DNA controls for all but one of the mutations, for which a synthetic control was used. All mutations were readily detected except for a duplication causing restrictive dermopathy where heterozygotes and homozygotes could only be distinguished by sequencing. Blinded testing of 12 additional samples from healthy Hutterites was performed by Asper Biotech using chip testing. All known mutations from previous molecular testing were detected on the chip. As well, additional mutations identified by the chip in these 12 samples were subsequently verified by a second method. CONCLUSIONS: Our analysis indicates that the chip is a sensitive and specific means of carrier testing in the Hutterite population and can serve as a model for other founder populations.

The use of ancestral haplotypes in the molecular diagnosis of familial breast cancer.

Mutations in BRCA1 and BRCA2 account for about 40% of families with an inherited susceptibility to breast and/or ovarian cancer. Mutational analysis of these two genes has become the standard of care for families with a strong suggestion of inherited susceptibility. Methodologies for screening vary, but one of the more popular techniques is dHPLC, due to its combination of high sensitivity and low cost. The presence of a large number of polymorphisms in the two BRCA genes complicates dHPLC analysis, often leading to complex elution profiles. There are concerns that a pattern produced by a sample heterozygous for a polymorphism may be very similar to that produced by a sample heterozygous for a unique mutation within the same amplicon. Further molecular analysis is often required to resolve whether any given shift is due to a polymorphism or a disease-causing mutation. The use of ancestral haplotypes was explored as a means to minimize the need for further analysis. Groups of 86 patients were genotyped for 12 BRCA1 polymorphisms or 20 BRCA2 polymorphisms. For BRCA1, eight distinct haplotypes were identified, which are largely derivatives of two main lineages. For BRCA2, 17 distinct haplotypes were identified, leading to a much more complex polymorphic pattern. With this knowledge, we have defined a system to determine which patients, if any, require further investigations. This method could be used to supplement any comprehensive screening methodology for other large genes that lie within strong regions of linkage disequilibrium such as NF1, CFTR, MLH1, or MSH2.