Tumour evolution inferred by single-cell sequencing

Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be lost that would be useful for reconstructing evolutionary history. Here we show that with flow-sorted nuclei, whole genome amplification and next generation sequencing we can accurately quantify genomic copy number within an individual nucleus. We apply single-nucleus sequencing to investigate tumour population structure and evolution in two human breast cancer cases. Analysis of 100 single cells from a polygenomic tumour revealed three distinct clonal subpopulations that probably represent sequential clonal expansions. Additional analysis of 100 single cells from a monogenomic primary tumour and its liver metastasis indicated that a single clonal expansion formed the primary tumour and seeded the metastasis. In both primary tumours, we also identified an unexpectedly abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to the metastatic site. In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates.     

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

Allele-specific DNA methylation (ASM) is a hallmark of imprinted genes, but ASM in the larger nonimprinted fraction of the genome is less well characterized. Using methylation-sensitive SNP analysis (MSNP), we surveyed the human genome at 50K and 250K resolution, identifying ASM as recurrent genotype call conversions from heterozygosity to homozygosity when genomic DNAs were predigested with the methylation-sensitive restriction enzyme HpaII. Using independent assays, we confirmed ASM at 16 SNP-tagged loci distributed across various chromosomes. At 12 of these loci (75%), the ASM tracked strongly with the sequence of adjacent SNPs. Further analysis showed allele-specific mRNA expression at two loci from this methylation-based screen--the vanin and CYP2A6-CYP2A7 gene clusters--both implicated in traits of medical importance. This recurrent phenomenon of sequence-dependent ASM has practical implications for mapping and interpreting associations of noncoding SNPs and haplotypes with human phenotypes.     

Nesting and summer habitat use by translocated Sage Grouse ( Centrocercus Urophasianus ) in central Idaho

We translocated 196 Sage Grouse ( Centrocercus urophasianus into Sawtooth Valley, Idaho, during March-April 1986-87 to augment a small resident population. Forty-four grouse equipped with radio transmitters were monitored through spring and summer. Nest sites ( n = 6) had greater ( P = .032) horizontal cover than did independent random plots ( n = 7). During summer, grouse used sites ( n = 50) with taller live and dead shrub heights, greater shrub canopy cover, and more ground litter ( P n = 50) 50-300 m from use sites. Distance to edge and mountain sagebrush ( Artemisia tridentata vaseyana ) density best separated use sites from independent random plots in logistic regression analysis and correctly classified 64% of the use sites and 78% of the independent random plots. Sage Grouse used sties that had narrower frequency distributions for many variables than did independent plots ( P < .04), suggesting selection for uniform habitat.     

Dispersal and extraterritorial movements of swift foxes ( Vulpes velox ) in northwestern Texas

Dispersal plays an important role in the population dynamics of many carnivores, yet little information exists about the dispersal and movement patterns of swift foxes ( Vulpes velox ). We radio-collared and monitored 68 swift foxes for dispersal at 2 study sites in northwestern Texas from January 2002 to April 2004. Dispersal distance for juveniles (13.1 ± 0.3 km, s ), adults (10 ± 4.7 km) and transients (25.4 ± 9.1 km) did not differ by age class ( F = 1.49, df = 2, P = 0.24) or sex ( F = 0.23, df = 1, P = 0.63) but differed by study site ( F = 4.72, df = 1, P = 0.04). Mean dispersal distance from private ranches (PR) was greater than from National Grasslands (NG). Peak dispersal occurred during October– November (13 individuals) and January–February (7 individuals). Dispersal direction was influenced by land-use practices (i.e., toward rangelands and away from anthropogenic features). Direction of dispersal among foxes that occupied the NG was uniform ( n = 16, P = 0.08), whereas foxes from PR dispersed in a northwesterly direction ( n = 18, P ≤ 0.001) away from a town and croplands. Three resident adult foxes made extraterritorial movements. Distances of these movements ranged from 0.2 km to 11.4 km. Distance of extraterritorial movements did not differ by sex ( F = 0.05, P = 0.83), nor by duration of movement ( F = 1.11, P = 0.32). Knowledge of movement distances and patterns is important for conservation and protection of swift foxes and their habitats.     

The NCBI dbGaP database of genotypes and phenotypes

The National Center for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.     

Nesting and brood-rearing characteristics of Chukars in west central Idaho

We analyzed attributes from 23 nests (10 renests) and 46 brood locations of radio-marked Chukars ( Alectoris chukar ) in the lower Salmon River canyon of west central Idaho in 1995 and 1996. Nesting effort was 100%, apparent nest success was 45%, and estimated time from destruction or abandonment of a nest to initiation of laying a subsequent nest averaged 13 ± 5 days s x . Average clutch size for 1st nests (14.5 ± 1.0) was greater ( P = 0.017) than renests (10.4 ± 1.1). Cover types used by nesting Chukars included grass/forb (48% of nests), rock (43%), and shrub (9%), whereas the most common structure used for nests was rock outcrop (57%). Chukars did not use yellow starthistle ( Centaurea solstitialis ) habitats differently from what was expected ( P = 0.08) for nesting, but birds with broods selected areas with less starthistle ( P < 0.001). Chukar broods, which averaged 12.0 ± 1.1 chicks, used shrub and grass/forb cover types approximately equally (43% and 47% of locations, respectively) but rock habitats infrequently (11%).     

Home range and seasonal movements of Columbian Sharp-tailed Grouse associated with Conservation Reserve Program and mine reclamation

During 1999 and 2000 we trapped and radio-marked 156 Columbian Sharp-tailed Grouse ( Tympanuchus phasianellus columbianus ) on leks in Conservation Reserve Program (CRP, n = 73) and mine reclamation (MR, n = 83) lands in northwestern Colorado. Median spring--fall home range sizes using the 95% fixed kernal and minimum convex polygon estimators for 54 grouse were 86 ha and 61 ha, respectively. Median fixed kernal home range size did not differ between males (79 ha) and females (87 ha). Home ranges of grouse associated with CRP (112 ha) were larger than those of grouse in MR (75 ha). Directional orientation of movements from leks of capture to wintering areas was nonrandom, and there was a positive elevation gain (median = 102 m) associated with these movements. Movements did not differ between grouse captured in CRP and MR for any season but did differ between genders for the spring--fall period. Males exhibited stronger fidelity and less variation in their movements than females; 96% of males compared with only 77% of females remained within 2.0 km of their lek of capture from spring through fall. Ninety percent of females nested within 2.5 km of their lek of capture. During winter all grouse were found farther (median = 21.5 km) from lek sites than in any other season. Males remained on the breeding range longer in the fall and returned earlier in the spring than females even though they wintered similar distances away (median males = 21.5 km, median females = 21.4 km). Our findings support the 2.0-km radius used in the Habitat Suitability Index model for Columbian Sharptailed Grouse to assess nest and brood-rearing cover around leks, but not the 6.5-km radius used to evaluate winter cover.     

Diet similarity between elk and deer in Utah

Growing numbers of elk ( Cervus elaphus ) on winter ranges might adversely affect sympatric wintering mule deer ( Odoeoileus hemionus ) if diets of the two species are similar. Diets of elk and deer on a northern Utah range were analyzed for overlap in winter with microhistological analysis of fecal samples. Diets overlapped 71%. No significant difference was found in use of grasses or shrubs between elk and deer; however, use of forbs was significantly different. Shrubs comprised the largest proportion of the diets of both elk and deer. Deer might be under more severe dietary stress than elk on poor winter ranges.