We have evaluated the extent to which SNPs identified by genomewide surveys as showing unusually high levels of population differentiation in humans have experienced recent positive selection, starting from a set of 32 nonsynonymous SNPs in 27 genes highlighted by the HapMap1 project. These SNPs were genotyped again in the HapMap samples and in the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) panel of 52 populations representing worldwide diversity; extended haplotype homozygosity was investigated around all of them, and full resequence data were examined for 9 genes (5 from public sources and 4 from new data sets). For 7 of the genes, genotyping errors were responsible for an artifactual signal of high population differentiation and for 2, the population differentiation did not exceed our significance threshold. For the 18 genes with confirmed high population differentiation, 3 showed evidence of positive selection as measured by unusually extended haplotypes within a population, and 7 more did in between-population analyses. The 9 genes with resequence data included 7 with high population differentiation, and 5 showed evidence of positive selection on the haplotype carrying the nonsynonymous SNP from skewed allele frequency spectra; in addition, 2 showed evidence of positive selection on unrelated haplotypes. Thus, in humans, high population differentiation is (apart from technical artifacts) an effective way of enriching for recently selected genes, but is not an infallible pointer to recent positive selection supported by other lines of evidence.

The human population has increased greatly in size in the last 100,000 years, but the initial stimuli to growth, the times when expansion started, and their variation between different parts of the world are poorly understood. We have investigated male demography in East Asia, applying a Bayesian full-likelihood analysis to data from 988 men representing 27 populations from China, Mongolia, Korea, and Japan typed with 45 binary and 16 STR markers from the Y chromosome. According to our analysis, the northern populations examined all started to expand in number between 34 (18–68) and 22 (12–39) thousand years ago (KYA), before the last glacial maximum at 21–18 KYA, while the southern populations all started to expand between 18 (6–47) and 12 (1–45) KYA, but then grew faster. We suggest that the northern populations expanded earlier because they could exploit the abundant megafauna of the “Mammoth Steppe,” while the southern populations could increase in number only when a warmer and more stable climate led to more plentiful plant resources such as tubers.

A major problem, especially the multidrug resistance, in chemotherapy was the resistance to the chemotherapeutic agents. ATP-binding cassette transporter superfamily that mediated the efflux of drugs was involved in multidrug resistance. In order to understand the relationship between the resistance to MTX and the transport protein superfamily of ATP-binding cassette, and to investigate the mechanism of resistance to MTX, the study detected the expressions of mdr1, mrp1, mrp2, mrp3, mrp5, mrp6 and abcg2 that encoded the transport proteins by SuperArray analysis and the expressions of MRP1and MRP5 proteins by Western blot analysis. The results showed that the multidrug resistance proteins were the chief member of ATP-binding cassette transporter superfamily related to resistance to MTX. And the high expression levels of mrp1 and mrp5 were detected. Moreover, it revealed by SuperArray analysis that expression of mrp5 in MTX-resistant cells was significantly higher than that in normal mouse cells. Besides, corresponding excessive expression of MRP5 protein in MTX-resistant cells was also confirmed by Western blot. So, MRP5 could play important roles in the resistance to MTX and would be a new potential drug target.

Mutations in the tumor suppressor gene transforming growth factor beta (TGFB) Type II receptor (TGFBR2) are frequently found in many cancers with microsatellite instability, but are less common in lung cancer. In the present study, we looked for mutations in TGFBR2 in nonsmall cell lung carcinoma (NSCLC) cells and tissues. A novel homozygous microdeletion (c.492_507del) was identified in two cell lines derived from the same giant cell carcinoma (GCC) and was confirmed in the corresponding tumor tissues. Furthermore, a heterozygous c.492_507del was found in the germ-line of one patient, as well as in the other GCC cases and some large cell carcinomas (LCC) but not in other subtypes of NSCLC. The 16bp-microdeletion introduced a premature stop codon at positions 590-592 of the cDNA, resulting in a truncated TGFBR2 protein with a mutated transmembrane domain and loss of kinase domain. The GCC cells were characterized as being unresponsive to TGFB induction both in growth inhibition and stimulation of extracellular matrix protein. Moreover, after the reconstitution of wild-type TGFBR2 expression, the sensitivity to TGFB was restored. Therefore, mutated TGFBR2 seems to play an important role in the abrogation of TGFB signal transduction in GCC cells. (c) 2006 Wiley-Liss, Inc.

We have identified a Y-chromosomal lineage that is unusually frequent in northeastern China and Mongolia, in which a haplotype cluster defined by 15 Y short tandem repeats was carried by approximately 3.3% of the males sampled from East Asia. The most recent common ancestor of this lineage lived 590 +/- 340 years ago (mean +/- SD), and it was detected in Mongolians and six Chinese minority populations. We suggest that the lineage was spread by Qing Dynasty (1644-1912) nobility, who were a privileged elite sharing patrilineal descent from Giocangga (died 1582), the grandfather of Manchu leader Nurhaci, and whose documented members formed approximately 0.4% of the minority population by the end of the dynasty.

The distribution of the MSY2 polymorphism in Chinese populations was analyzed by PCR. The results showed that the MSY2*4 allele, whose frequency in the total material was found to be 94.95%, was the common allele, while the distribution of the MSY2*3 allele was significantly different in the 416 tested males from the 9 populations under study. Based on the chi2-analysis, a distinct diversity was found in the non-group populations. Diversities were also discovered between southern and northern groups and among southern groups. On the contrary, no difference concerning the diversity was detected among the northern populations. In conclusion, MSY2 proved to be an important genetic marker with regard to the study of the genetic structure of Chinese populations, and further evidence is given concerning the migration direction between South and North.

OBJECTIVE:To analyze the genetic polymorphism of 15 single nucleotide polymorphism (SNP) loci on the nonrecombining portion of the Y chromosome in 6 populations in China.METHODS:Allelic specific polymerase chain reaction and 2% agarose gel electrophoresis and 6% PAGE were used to analyze the genetic polymorphism of 343 unrelated males, representing 6 populations in China, including Fujian Hans, Sichuan Hans, Mongolian, Hezhen, Sibo and Hui from the South, Northeast and Northwest.RESULTS:Thirty haplogroups were observed, and 3 of them (H15, H16, H18) were seen in all of the six populations. Although the heterozygosity levels of the Hezhen, Mongolian, Sibo populations are similar and those of the other 3 populations (Fujian Hans, Sichuan Hans, Hui) are similar, the pairwise differences among haplogroups are significant. Analysis of molecular variance (AMOVA) and principal component (PC) analysis of the haplogroup distributions suggested highly different allele diversity between group I including Hezhen, Mongolian, Sibo and group II including Hui, Fujian Hans, Sichuan Hans.CONCLUSION:The above analyses show more significant variance components in Northeast/South populations and clearly reveal the geographic genetic relationship among the six populations in the Northeast/Northwest/South. These results confirm the complexity of the genetic structure of Chinese populations and make a significant contribution for constructing the contemporary human gene pool and tracing genetic dispersal trail from Chinese populations.

Ancient demographic events can be inferred from the distribution of biallelic polymorphisms of NRY. In our study, six Y-biallelic markers were screened in 326 Y-chromosomes from five Chinese populations: Manchu, Fujian Han, Kazak, Bouyei and Sichuan Han. The chi2-test was performed using the SAS package. ARLEQUIN and SPSS programs were used for pairwise Fst's and genetic clusters, respectively. The M9 (G) and RPS4Y (T) polymorphisms show greater variance in these five populations and are informative and sensible in Chinese population genetic research, while the other four are less polymorphic. Significant differences in the distribution of the six biallelic markers were found between the three southern groups and the two northern groups involved in the present study. The Kazak population demonstrated marked differences not only from the southern populations, but differed notably from the other northern population, the Manchu. This result clearly suggests that the original division of the investigated groups into north and south would not yield optimal results from which useful generalizations could be made. The results have proven to be extremely useful, their analysis not only brought to light important new facts on the population structures, but supplied also useful guidelines for further additional Chinese population genetic research projects.

Objective To investigate common chromosomal changes and the LOH frequency of microsatellite loci in primary gastric cancer samples in order to locate the deleted regions in which human gastric cancer related genes might exist.Methods Comparative genomic hybridization (CGH) was used to define global chromosomal aberrations in 43 primary gastric tumors. Based on the results of CGH, analysis of loss of heterozygosity (LOH) was performed in chromosome 19 in which the loss was first discovered in the gastric cancers. The PCR-based approach was used to investigate 22 loci, which are spaced at 1.1-10.9 cM intervals throughout chromosome 19. The amplified PCR fragments were subjected to electrophoresis in PAGE gel and analyzed with GenescanTM and GenotyperTM. Results CGH analysis revealed gains in chromosome 3p(8/43), 8q(8/43), 20 [20 (9/43), 20p(7/43), 20q(4/43)], 12q(16/43), 13q(12/43) and losses in 19 [19 (15/43)], 7 [17 (8/43), 17p (10/43)], 16 (10/43) and 1p (11/43). Among the 43 evaluated samples, the most frequent LOH was detected at locus D19S571 (27.81%). Conclusions The tumorigenesis of gastric cancer includes several chromosomal changes. The aberration of chromosome 19 was the first common change founded in gastric cancer. The region near the D19S571 might harbor potential genes related to the tumorigenesis of gastric cancer.

Many researches have been done concerning a C→T mutation at nucleotide position 677 in exon 3 of the methylenetetrahydrofolate reductase (MTHFR) gene which changes alanine to valine [1]. Here we report the MTHFR C677T mutation rate in five Chinese populations: Han nationality, Oroqen, Ewenki, Daur and Zhuangzu for the first time in the world. The relationship between this mutation and some diseases, such as coronary heart disease and neural tube defects is also explored.

Fifty-seven primary squamous cell carcinomas of the lung were analyzed cytogenetically. Karyotyping was possible in seven cases, and chromosome counting without detailed analysis was possible in 16 other cases. The results suggested that structural chromosome rearrangements related to the short arms of chromosomes 1(5/7), 9(3/7), and 11(6/7), and the long arms of chromosomes 6(4/7) and 7(6/7) may be the primary and non-random chromosome defects which are closely associated with human lung squamous cell carcinoma. These primary and non-random chromosome defects are believed to confer a proliferative advantage to cells carrying them, and to be involved in the pathogenesis of human lung squamous cell carcinoma.

Isochromosomes related to chromosomes 1, 5, 6, 8, and 9 were frequently observed in 23 cases of lung cancer. Their existence in tumor cells might be nonrandom. Premature centromere separation (PCS) was found in the PGT-131 cell line of a lung cancer. It is suggested that PCS may play a role in the formation of isochromosomes in lung cancer.

Direct chromosome analyses were performed in 50 cases of primary breast carcinoma. Thirty-six cases had modal chromosome counts in the diploid range; the other 14 cases were polyploid. Of the 22 cases with detailed G-banding analyses, the most frequent structural changes involved chromosome 1 (15 of 22), 3 (13 of 22), and 6 (13 of 22). Deletion of chromosome 1p was noted in nine cases, and both 3p- and 6q- were noted in 10 cases.

In direct preparation of five primary esophageal cancers, chromosomes 1, 3, and 12 were most frequently involved in structural abnormalities; 12p- was consistently seen in all five cases and, thus, could be considered as one of the characteristic chromosome changes in esophageal cancer. Moreover, 2p-, 4p-, and 7q- were seen in three cases.

G-banded karyotypes were analyzed on four human lung adenocarcinoma cell lines, AGZY83-a, LTEP-a1, LTEP-a2, and GLC-82. More than 50 cells were counted and 20-40 cells were karyotyped for each cell line at different passages. The chromosome numbers of cell line AGZY83-a, LTEP-a1, LTEP-a2, and GLC-82 were 53-69, 100-110, 51-56, and 61-63, respectively. Each cell line had a number of markers involving complex chromosome rearrangements. Chromosomal analysis at different passages showed the stability of these cell lines in vitro. It was revealed that the marker chromosomes involving deletions or rearrangements of the short arm of chromosome #1 were present in all the four cell lines with breakpoints at 1p12-1p22.