Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals

The recent hapmap effort has placed focus on the application of genome-wide SNP analysis to assess the contribution of genetic variability, particularly SNPs, to traits such as disease. Here, we describe the utility of genome-wide SNP analysis in the direct detection of extended homozygosity and structural genomic variation. We use this approach to assess the frequency of genomic alterations resulting from the lymphoblast immortalization and culture processes commonly used in cell repositories. We have assayed 408 804 SNPs in 276 DNA samples extracted from Epstein-Barr virus immortalized cell lines, which were derived from lymphocytes of elderly neurologically normal subjects. These data reveal extended homozygosity (contiguous tracts >5 Mb) in 9.5% (26/272) and 340 structural genomic alterations in 182 (66.9%) DNA samples assessed, 66% of which did not overlap with previously described structural variations. Examination of DNA extracted directly from the blood of 30 of these subjects confirmed all examined instances of extended homozygosity (6/6), 75% of structural genomic alteration <5 Mb in size (12/16) and 13% (1/8) of structural genomic alteration >5 Mb in size. These data suggest that structural genomic variation is a common phenomenon in the general population. While a proportion of this variability may be caused or its relative abundance altered by the immortalization and clonal process this will have only a minor effect on genotype and allele frequencies in a large cohort. It is likely that this powerful methodology will augment existing techniques in the identification of chromosomal abnormalities.

Heart disease associated with deletion of the short arm of chromosome 18

Deletion of the short arm of chromosome 18 provides a highly variable phenotype. Mental retardation, short stature, and abnormal facies are invariably present. About 9 percent of patients with this syndrome have cardiac pathology. An additional case with congenital heart disease has been presented along with a review of the literature concerning the association of congenital heart disease and the 18p- syndrome.

Familial erythroleukemia: four cases of the Diguglielmo syndrome in close relatives

Erythroleukemia was diagnosed in three brothers during a 6-month period in 1976. A son of one leukemic had died 5 years earlier with erythroleukemia. First-degree relatives of these men were evaluated in an attempt to identify contributing factors. Twenty-four relatives have been studied. Immunoglobulin M was elevated in 14 of 16 persons (mean, 352.8 mg/dl; normal, less than 145 mg/dl; P less than .001). This was neither a monoclonal protein nor rheumatoid factor. Age-dependent red cell enzymes were increased. Erythrocyte hexokinase was markedly increased in 23 of 24 persons (mean, 35.05 units/100 ml RBC; normal, less than 18 units; P less than .001). Evidence for a hemolytic state was absent. Bone marrow samples in 8 first-degree relatives were normal. Cytogenetics were normal in 18 relatives. One leukemic exhibited hypoploidy and a marker chromosome. The association of an immunoglobulin abnormality and enzymopathy in the leukemics and relatives alike suggests a hereditary susceptibility to the development of erythroleukemia. The exact link is not identified.