Genotyping for genetic association studies: Methods and applications

In this thesis, two separate single nucleotide polymorphism (SNP) genotyping techniques were set up at the Finnish Genome Center, pooled genotyping was evaluated as a screening method for large-scale association studies, and finally, the former approaches were used to identify genetic factors predisposing to two distinct complex diseases by utilizing large epidemiological cohorts and also taking environmental factors into account. The first genotyping platform was based on traditional but improved restriction-fragment-length-polymorphism (RFLP) utilizing 384-microtiter well plates, multiplexing, small reaction volumes (5 µl), and automated genotype calling. We participated in the development of the second genotyping method, based on single nucleotide primer extension (SNuPeTM by Amersham Biosciences), by carrying out the alpha- and beta tests for the chemistry and the allele-calling software. Both techniques proved to be accurate, reliable, and suitable for projects with thousands of samples and tens of markers. Pooled genotyping (genotyping of pooled instead of individual DNA samples) was evaluated with Sequenom s MassArray MALDI-TOF, in addition to SNuPeTM and PCR-RFLP techniques. We used MassArray mainly as a point of comparison, because it is known to be well suited for pooled genotyping. All three methods were shown to be accurate, the standard deviations between measurements being 0.017 for the MassArray, 0.022 for the PCR-RFLP, and 0.026 for the SNuPeTM. The largest source of error in the process of pooled genotyping was shown to be the volumetric error, i.e., the preparation of pools. We also demonstrated that it would have been possible to narrow down the genetic locus underlying congenital chloride diarrhea (CLD), an autosomal recessive disorder, by using the pooling technique instead of genotyping individual samples. Although the approach seems to be well suited for traditional case-control studies, it is difficult to apply if any kind of stratification based on environmental factors is needed. Therefore we chose to continue with individual genotyping in the following association studies. Samples in the two separate large epidemiological cohorts were genotyped with the PCR-RFLP and SNuPeTM techniques. The first of these association studies concerned various pregnancy complications among 100,000 consecutive pregnancies in Finland, of which we genotyped 2292 patients and controls, in addition to a population sample of 644 blood donors, with 7 polymorphisms in the potentially thrombotic genes. In this thesis, the analysis of a sub-study of pregnancy-related venous thromboses was included. We showed that the impact of factor V Leiden polymorphism on pregnancy-related venous thrombosis, but not the other tested polymorphisms, was fairly large (odds ratio 11.6; 95% CI 3.6-33.6), and increased multiplicatively when combined with other risk factors such as obesity or advanced age. Owing to our study design, we were also able to estimate the risks at the population level. The second epidemiological cohort was the Helsinki Birth Cohort of men and women who were born during 1924-1933 in Helsinki. The aim was to identify genetic factors that might modify the well known link between small birth size and adult metabolic diseases, such as type 2 diabetes and impaired glucose tolerance. Among ~500 individuals with detailed birth measurements and current metabolic profile, we found that an insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was associated with the duration of gestation, and weight and length at birth. Interestingly, the ACE insertion allele was also associated with higher indices of insulin secretion (p=0.0004) in adult life, but only among individuals who were born small (those among the lowest third of birth weight). Likewise, low birth weight was associated with higher indices of insulin secretion (p=0.003), but only among carriers of the ACE insertion allele. The association with birth measurements was also found with a common haplotype of the glucocorticoid receptor (GR) gene. Furthermore, the association between short length at birth and adult impaired glucose tolerance was confined to carriers of this haplotype (p=0.007). These associations exemplify the interaction between environmental factors and genotype, which, possibly due to altered gene expression, predisposes to complex metabolic diseases. Indeed, we showed that the common GR gene haplotype associated with reduced mRNA expression in thymus of three individuals (p=0.0002).

Studies on crystalline complexes involving amino acids. V. The structure of L-serine-L-ascorbic acid

L-Serine-L-ascorbic acid, C3HTNOa. C6HsO6, a 1:1 complex between the amino acid serine and the vitamin ascorbic acid, crystallizes in the orthorhombic space group P2~2~2~ with four formula units in a cell of dimensions a = 5.335(3), b = 8.769(2), c = 25.782 (5) A. The structure was solved by direct methods and refined by full-matrix least squares to an R of 0.036 for 951 observed reflections. Both molecules are neutral in the structure. The conformation of the serine molecule is different from that observed in the crystal structures of L-serine, DL-serine and L-serine monohydrate. The enediol group in the ascorbic acid molecule is planar, whereas significant departures from planarity are observed in the lactone group. The conformation of this molecule is similar to that observed in arginine ascorbate. The unlike molecules aggregate into separate columns in the crystal structure. The columns are held together by hydrogen bonds. Among these, a pair of hydrogen bonds between the enediol group of ascorbic acid and the carboxylate group of serine provides a possible model for a specific interaction between ascorbic acid and a carboxylate ion.

Influence of Band Non-Parabolicity on Few Ballistic Properties of III-V Quantum Wire Field Effect Transistors Under Strong Inversion

A simplified yet analytical approach on few ballistic properties of III-V quantum wire transistor has been presented by considering the band non-parabolicity of the electrons in accordance with Kane's energy band model using the Bohr-Sommerfeld's technique. The confinement of the electrons in the vertical and lateral directions are modeled by an infinite triangular and square well potentials respectively, giving rise to a two dimensional electron confinement. It has been shown that the quantum gate capacitance, the drain currents and the channel conductance in such systems are oscillatory functions of the applied gate and drain voltages at the strong inversion regime. The formation of subbands due to the electrical and structural quantization leads to the discreetness in the characteristics of such 1D ballistic transistors. A comparison has also been sought out between the self-consistent solution of the Poisson's-Schrodinger's equations using numerical techniques and analytical results using Bohr-Sommerfeld's method. The results as derived in this paper for all the energy band models gets simplified to the well known results under certain limiting conditions which forms the mathematical compatibility of our generalized theoretical formalism.

Gurs: 'Stamps' from the concentration camp,q-v.

The designs are drawn in the miniature style of postage stamps and include mock postage prices. Presumably this method was inspired by the shortage of paper at the camp in Gurs, Southern France, where these works were done; but specially this format is also used to stress the irony of the content, especially in the trio of design marked "Liberte-Egalite-Fraternite", aside from one marked "Avion de Gurs", all others are labelled simply " Gurs ", at the bottom as if this were the country of origin of a postal system.

Plan U.S.R.R. Melitopol'skogo okruga Genicheskogo raiona poluostrova Chongar vymezhevannogo v poriadke chastichnogo izmeneniia ustroistva kolfonda s ustroistvom poselkov, razbivkoiu na polia sevooborota, gony soglasno nakazu N.K.Z dnia 1927, n 52-2825. Izmerenie v nature proizvedeno i plan etot sostovlen X. partieiu po ustroistvu kolfondov

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Skhematicheskii plan uchastkov pereselencheskogo fonda v Krymu

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Sostoianie posevov v raionakh evreiskogo zemledeliia na 15-oe iiunia 1927 goda

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Meditsinskie uchastki v evreiskikh koloniiakh Khersonskogo u Kr.Rozhskogo raionov

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Vykopirovka plana Melitopol'skogo okruga Genicheskovo raiona poluostrova Chongar otgranichennogo v poriadke ustroistva Kolfonda s obrazovaniem posëlkov i rozbivkoiu na polia sevooborota goni, sogliasno plana zemleustraitelnykh rabot po 1925-1926 gg.; plan sostavlen 9 partiei po ustroistvu kolfonda

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Proekt otvoda zemli "Komzetu" po Sary-Bulatskoi dachi razverstaniia Evpatoriiskogo raiona v 1930 godu

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Vykopirovka iz obshchego plana Biiuk-Onlarskoi dachi razverstaniia na uchastok, otvedennyi KOMZET-u pri der. Lenindorf, vkliuchennyi v obshchii sevooborotom s der. Ochka-Boiliar

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Vykopirovka s plana Seĭtlerskoĭ dachi razverstani︠ia︡ Kr.A.S.SD.R., na uchastok zemli otvedennyĭ KOMZET'u (Beǐs-Lekhem), pri provedenii rabot po zemreforme v 1930 g.

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Vykopirovka s plana Seĭtlerskoĭ dachi razverstani︠ia︡, Kr.A.S.SD.R., na uchastok zemli otvedennyĭ KOMZET'u (s -Kh. ART. "Rabotnik" - Aranda), pri provedenii rabot po zemreforme v 1930 g.

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