We have developed a DNA tag sequencing and mapping strategy called gene identification signature (GIS) analysis, in which 5' and 3' signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene. GIS analysis is potentially 30-fold more efficient than standard cDNA sequencing approaches for transcriptome characterization. We demonstrated this approach with 116,252 PET sequences derived from mouse embryonic stem cells. Initial analysis of this dataset identified hundreds of previously uncharacterized transcripts, including alternative transcripts of known genes. We also uncovered several intergenically spliced and unusual fusion transcripts, one of which was confirmed as a trans-splicing event and was differentially expressed. The concept of paired-end ditagging described here for transcriptome analysis can also be applied to whole-genome analysis of cis-regulatory and other DNA elements and represents an important technological advance for genome annotation.

Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.

BackgroundEfforts to assess the burden of non-communicable diseases risk factors has improved in low and middle-income countries after political declaration of UN High Level Meeting on NCDs. However, lack of reliable estimates of risk factors distribution are leading to delay in implementation of evidence based interventions in states of India.MethodsA STEPS Survey, comprising all the three steps for assessment of risk factors of NCDs, was conducted in Punjab state during 2014–15. A statewide multistage sample of 5,127 residents, aged 18–69 years, was taken. STEPS questionnaire version 3.1 was used to collect information on behavioral risk factors, followed by physical measurements and blood and urine sampling for biochemical profile.ResultsTobacco and alcohol consumption were observed in 11.3% (20% men and 0.9% women) and 15% (27% men and 0.3% women) of the population, respectively. Low levels of physical activity were recorded among 31% (95% CI: 26.7–35.5) of the participants. The prevalence of overweight and obesity was 28.6% (95% CI: 26.3–30.9) and 12.8% (95% CI: 11.2–14.4) respectively. Central obesity was higher among women (69.3%, 95% CI: 66.5–72.0) than men (49.5%, 95% CI: 45.3–53.7). Prevalence of hypertension in population was 40.1% (95% CI: 37.3–43.0). The mean sodium intake in grams per day for the population was 7.4 gms (95% CI: 7.2–7.7). The prevalence of diabetes (hyperglycemia), hypertriglyceridemia and hypercholesterolemia was 14.3% (95% CI: 11.7–16.8), 21.6% (95% CI: 18.5–25.1) and 16.1% (95% CI: 13.1–19.2), respectively. In addition, 7% of the population aged 40–69 years had a cardiovascular risk of ≥ 30% over a period of next 10 years.ConclusionWe report high prevalence of risk factors of chronic non-communicable diseases among adults in Punjab. There is an urgent need to implement population, individual and programme wide prevention and control interventions to lower the serious consequences of NCDs.

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The high rate of recurrence of breast cancer argues for the development of interventions that can prevent or delay the onset of metastatic disease. These estimates of lifetime costs and the methodology on which they are based can be used to evaluate the cost-effectiveness of such secondary prevention strategies. These estimates also can serve as a benchmark against which the lifetime costs of treating other diseases can be assessed.