RHD positive haplotypes in D negative Europeans

BACKGROUND: Blood group genotyping is increasingly utilized for prenatal diagnosis and after recent transfusions, but still lacks the specificity of serology. In whites, the presence of antigen D is predicted, if two or more properly selected RHD-specific polymorphism are detected. This prediction must fail, if an antigen D negative RHD positive allele is encountered. Excluding RHDψ and Cde(S) frequent only in individuals of African descent, most of these alleles are unknown and the population frequency of any such allele has not been determined. METHODS: We screened 8,442 antigen D negative blood donations by RHD PCR-SSP. RHD PCR positive samples were further characterized by RHD exon specific PCR-SSP or sequencing. The phenotype of the identified alleles was checked and their frequencies in Germans were determined. RESULTS: We detected 50 RHD positive samples. Fifteen samples harbored one of three new D(el) alleles. Thirty samples were due to 14 different D negative alleles, only 5 of which were previously known. Nine of the 14 alleles may have been generated by gene conversion in cis, for which we proposed a mechanism triggered by hairpin formation of chromosomal DNA. The cumulative population frequency of the 14 D negative alleles was 1:1,500. Five samples represented a D(+/-) chimera, a weak D and three partial D, which had been missed by routine serology; two recipients transfused with blood of the D(+/-) chimera donor became anti-D immunized. CONCLUSION: The results of this study allowed to devise an improved RHD genotyping strategy, the false-positive rate of which was lower than 1:10,000. The number of characterized RHD positive antigen D negative and D(el) alleles was more than doubled and their population frequencies in Europe were defined

Embryonic Morphogen Nodal Promotes Breast Cancer Growth and Progression

Breast cancers expressing human embryonic stem cell (hESC)-associated genes are more likely to progress than well-differentiated cancers and are thus associated with poor patient prognosis. Elevated proliferation and evasion of growth control are similarly associated with disease progression, and are classical hallmarks of cancer. In the current study we demonstrate that the hESC-associated factor Nodal promotes breast cancer growth. Specifically, we show that Nodal is elevated in aggressive MDA-MB-231, MDA-MB-468 and Hs578t human breast cancer cell lines, compared to poorly aggressive MCF-7 and T47D breast cancer cell lines. Nodal knockdown in aggressive breast cancer cells via shRNA reduces tumour incidence and significantly blunts tumour growth at primary sites. In vitro, using Trypan Blue exclusion assays, Western blot analysis of phosphorylated histone H3 and cleaved caspase-9, and real time RT-PCR analysis of BAX and BCL2 gene expression, we demonstrate that Nodal promotes expansion of breast cancer cells, likely via a combinatorial mechanism involving increased proliferation and decreased apopotosis. In an experimental model of metastasis using beta-glucuronidase (GUSB)-deficient NOD/SCID/mucopolysaccharidosis type VII (MPSVII) mice, we show that although Nodal is not required for the formation of small (\u3c100 cells) micrometastases at secondary sites, it supports an elevated proliferation:apoptosis ratio (Ki67:TUNEL) in micrometastatic lesions. Indeed, at longer time points (8 weeks), we determined that Nodal is necessary for the subsequent development of macrometastatic lesions. Our findings demonstrate that Nodal supports tumour growth at primary and secondary sites by increasing the ratio of proliferation:apoptosis in breast cancer cells. As Nodal expression is relatively limited to embryonic systems and cancer, this study establishes Nodal as a potential tumour-specific target for the treatment of breast cancer. © 2012 Quail et al

Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations

<p>Abstract</p> <p>Background</p> <p>Codon usage in genomes is biased towards specific subsets of codons. Codon usage bias affects translational speed and accuracy, and it is associated with the tRNA levels and the GC content of the genome. Spontaneous mutations drive genomes to a low GC content. Active cellular processes are needed to maintain a high GC content, which influences the codon usage of a species. Loss-of-function mutations, such as nonsense mutations, are the molecular basis of many recessive alleles, which can greatly affect the genome of an organism and are the cause of many genetic diseases in humans.</p> <p>Methods</p> <p>We developed an event based model to calculate the risk of acquiring nonsense mutations in coding sequences. Complete coding sequences and genomes of 40 eukaryotes were analyzed for GC and CpG content, codon usage, and the associated risk of acquiring nonsense mutations. We included one species per genus for all eukaryotes with available reference sequence.</p> <p>Results</p> <p>We discovered that the codon usage bias detected in genomes of high GC content decreases the risk of acquiring nonsense mutations (Pearson's <it>r </it>= -0.95; <it>P </it>< 0.0001). In the genomes of all examined vertebrates, including humans, this risk was lower than expected (0.93 ± 0.02; mean ± SD) and lower than the risk in genomes of non-vertebrates (1.02 ± 0.13; <it>P </it>= 0.019).</p> <p>Conclusions</p> <p>While the maintenance of a high GC content is energetically costly, it is associated with a codon usage bias harboring a low risk of acquiring nonsense mutations. The reduced exposure to this risk may contribute to the fitness of vertebrates.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Häufigkeit sporadischer nicht-funktionaler Allele und ihre Bedeutung für die Genotypisierung am Beispiel des Polymorphismus im FUT1-Blutgruppengen

Für die Genotypisierung werden gegenwärtig häufig PCR-gestützte Techniken benutzt, die kurze, sogenannte charakteristische beziehungsweise diagnostische Sequenzen nachweisen. Mit diesen Techniken kann der Phänotyp regelmäßig nicht korrekt vorhergesagt werden, wenn sporadische nicht-funktionale Allele angetroffen werden. Die Häufigkeit solcher sporadischer aberranter Allele und ihre dadurch bedingte Bedeutung für die Genotypisierung waren für kein Gen beim Menschen unter niedrigem Selektionsdruck bekannt. In der vorliegenden Arbeit wurde die Frequenz der sehr seltenen Bombay (0h)-Blutgruppe (Genotyp hh sese) in einer systematischen Suche unter mehr als 600.000 Blutspendern in Baden-Württemberg bestimmt. Die Ergebnisse dieser Studie zusammen mit molekularbiologischen Untersuchungen wurden ausgewertet, um die Populationsfrequenz nicht-funktionaler Allele am Beispiel des Gens zu bestimmen, das für die alpha(1,2)Fukosyltransferase kodiert (FUT1 oder H). Sieben unterschiedliche h-Allele wurden in fünf unverwandten Individuen gefunden. Die nachgewiesenen h-Allele unterschieden sich bei allen untersuchten Probanden. Drei der Probanden waren homozygot für ihr privates Allel. Es wurde kein prävalentes h Allel nachgewiesen. Im einzelnen wurden eine frame shift- und fünf missense-Mutationen gefunden, die wahrscheinlich die Null-Phänotypen verursachten. Die kodierende Sequenz eines h Allels war identisch mit der Sequenz des funktionalen H Allels. Der mittlere Konsanguinitätskoeffizient alpha war 0,00116. Die Frequenz der nicht-funktionalen Allele im FUT1-Gen wurde mit 1:367 in einer großen deutschen Population berechnet (95 Prozent-Konfidenzintervall: 1:185 - 1:824). Der Bombay (0h)-Phänotyp wird in der weißen Bevölkerung durch diverse, sporadische nicht-funktionale Allele verursacht. Es gibt kein prävalentes h-Allel. Unser Ansatz erlaubte zum ersten Mal eine direkte Kalkulation des Koeffizienten alpha für eine Population ohne Berücksichtigung von Verwandtschaftsverhältnissen. Unter der Annahme ähnlicher Häufigkeiten von nicht-funktionalen Allelen in anderen Glykosyltransferase-Genen, wie zum Beispiel in den Genen der AB0-Blutgruppe, können die gegenwärtigen Genotypisierungsstrategien Fehlerraten mit einer Häufigkeit von einem in ungefähr 300 Individuen der Blutgruppe 0 aufweisen. Sporadische neutrale Allele können ebenso ein erhebliches Problem für die populationsweite Genotypisierung vieler krankheitsassoziierter Gene darstellen