2009 Vienna - European Society of Human Genetics

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Prenatal and perinatal genetics P05.53 Rapid prenatal of chromosome aneuploidy by Qt-PcR J. Kasnauskiene1,2 , N. Krasovskaja2 , V. Kučinskas1,2 ; 1 2 Vilnius University, Vilnius, Lithuania, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania. QT-PCR can detect the great majority of chromosome abnormalities in prenatal samples being targeted to chromosomes 13, 18, 21 X and Y. It is a rapid robust and accurate test for the prenatal diagnosis of most frequent trisomies. Main advantages of the test: low cost, speed and automation large scale application. In Lithuania QT-PCR is as a standalone test for a sub-set of prenatal samples, with the aim of minimising the identification of chromosome abnormalities of unknown clinical significance and reducing double testing. All prenatal samples are tested for trisomies 13, 18, 21, X and Y chromosomes using QT-PCR. Katyotype analysis is carried out only for referrals with NT >3 mm before 14 weeks or >6 mm thereafter, ultrasound abnormalities (excluding single soft marker), from families with a previous chromosome abnormality (excluding single soft markers). During four years 1187 AF and 24 CVS were received. AF 22 % were karyotyped. 4.8 % AF and 4.2 % CVS were abnormal. All aneuploidies involving chromosomes 13, 18, 21, X and Y were detected with sensitivity and specificity 100%.Large scale application of QT-PCR has reduced the load of prenatal cytogenetics if all pregnancies are monitored by non invasive methods. P05.54 Molecular karyotyping of whole genome amplified samples H. Raussi1 , M. Mäkinen2 , S. Ruosaari1 , A. Godenhjelm1 , P. Ollikka1 ; 1 2 PerkinElmer Human Health, Turku, Finland, University Of Turku, Turku, Finland. Background: Array comparative genomic hybridization (array CGH) has been widely used for detection of copy number changes in tumors and genetic disorders. In the prenatal setting, however, where starting DNA amounts may be too low for array CGH, the feasibility of the technology remains to be defined. Although whole genome amplification (WGA) has potential for expanding the use of array CGH in analyses of few nanograms of DNA or even single cells, further information is needed about the putative bias WGA introduces to the genomic profiles. Methods: We performed WGA on DNA samples and analyzed the resulting genomic profiles by means of array CGH. The amplification was performed with GenomePlex ® (SigmaAldrich) products using few nanograms of DNA or few cells as a starting material. To assess possible bias introduced by WGA, the amplified test samples were hybridized using both the respective native and an amplified reference DNA as the reference. PerkinElmer’s Constitutional Chip ® platform and SpectralWare ® analysis software were used in the array CGH analysis. Results and conclusions: Our results indicate that the Constitutional Chip ® platform works effectively for generating array CGH data from amplified test and reference samples. However, when native DNA is compared against the respective amplified DNA, specific chromosome regions continuously fail to amplify, especially as the amount of the starting material is decreased. The results show that detection of aneuploidies is not hampered by the sequence drop-out, yet micro-level changes may be missed owing to the biased amplification. P05.55 Detection of fetal trisomies with a 19-plex QF-PcR using the novel Amplitaq Gold PcR 360 master mix R. Achmann1 , F. Stellmer1 , K. Held1 , H. Schulte1 , A. Sartori2 ; 1 2 MVZ genteQ, Hamburg, Germany, Applied Biosystems GmbH, Darmstadt, Germany. In recent years quantitative fluorescent polymerase chain reaction (QF-PCR) with short tandem repeat markers (STR) have become the method of choice for the prenatal detection of the most common chromosome aneuploidies. The main advantages of QF-PCR are its accuracy and speed. Typically test results can be obtained within a few hours after sample receipt. We established an elaborated multiplex QF-PCR covering the chromosomes 13, 18, 21 and X with a total of 19 polymorphic markers. Primers for amplification of markers were labeled with four different fluorescent dyes. PCR products were analyzed in parallel on a multicapillary electrophoresis instrument. We compared results obtained with our standard protocol using a chemically blocked hot start Taq polymerase with Applied Biosystems novel AmpliTaq Gold PCR 360 Master Mix. We were able to reduce cycling time from 2:45 hours to 2 hours with AmpliTaq Gold PCR 360 Master Mix without compromising the PCR yield, specificity and sensitivity. We observed reliable amplification of marker alleles allowing us to correctly deduce fetal chromosomal aneuploidies from amniotic fluid and ‘chorionic villus’ samples. P05.56 Quantitative analysis of foetal DNA in maternal circulation in gestational diabetes mellitus (GDm) pregnancies M. Zamanpoor1 , T. Karuppiah1 , R. Rosli1 , M. Yazid1 , Z. Husain2 ; 1Clinical Genetics Unit, Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia, 2Department of Interdisciplinary Medicine, BIDMC, Harvard Medical School, Boston, MA, United States. Gestational Diabetes Mellitus (GDM) is a condition in which women without prior diagnosis of diabetes, show high levels of blood glucose during pregnancy. GDM affects 3-10% of pregnancies. Studies have shown that women with GDM have a higher risk of preeclampsia and that their offsprings are at a higher risk for congenital malformations. Increased amount of cell free foetal DNA (cffDNA) in maternal plasma has been found in adverse pregnancies such as preeclampsia, gestational hypertension, foetal chromosomal aneuploidies, placental abnormalities, preterm labour and hyperemesis gravidarum. It was suggested that elevation of cffDNA in maternal plasma could be used for early identification of adverse pregnancies. The aim of our study was to determine the elevation of cffDNA levels in GDM pregnancies compared to normal pregnancies. In this study, twenty-three secondtrimester plasma samples from GDM pregnancies were compared with fourteen control samples of normal pregnancies, all carrying a singleton male foetus. The cffDNA concentrations were measured by quantitative real-time PCR amplification of SRY gene which is located on Y chromosome, using TaqMan dual labelled probe system. The mean of cffDNA levels for cases and controls were 3.47 and 5.64 genome equivalents/ml, respectively. No significant differences (P = 0.17) in the mean of cffDNA concentration were observed between GDM and normal pregnancies. In conclusion, GDM does not affect levels of maternal plasma cffDNA. Hence, if cffDNA is used as an additional serum marker in prenatal screening test in the future, our data suggests that cffDNA quantity will not require adjustment for GDM pregnancies. P05.57 Evaluation of automated DNA extraction for non invasive prenatal diagnosis using free fetal DNA in maternal plasma E. Ordoñez1 , L. Rueda1 , P. Cañadas1 , C. Mediano2 , C. Fuster3 , V. Cirigliano1 ; 1 2 General Lab, Barcelona, Spain, Hospital Vall d’Hebrón, Barcelona, Spain, 3Universitat Autònoma de Barcelona, Barcelona, Spain. The use of free fetal DNA for non invasive prenatal detection of fetal sex and RhD status is part of the daily routine in several genetic centers. Automation of DNA extraction process simplifies sample handling allowing high throughput of samples. We evaluated the suitability of using an automated DNA extraction procedure for ffDNA extraction in comparison with the most commonly used manual method. Fifty Blood samples collected in the first trimester of pregnancy from pregnant women with male fetuses were selected for this study. DNA extractions were performed by using 500µL of plasma for the QIAamp DSP Virus Kit (QIAgen Inc.) or 1mL of plasma for the COBAS AmpliPrep® DNA/RNA extractor from ROCHE. ffDNA was quantified by rtPCR amplification of the SRY gene and yield (GE/mL) was calculated for both extraction methods. SRY amplification was detectable in all samples independently from the extraction procedure and no false negative results were observed. ffDNA quantity obtained by the manual extraction method was higher than using the automated extraction with a mean of 259,43GE/mL and 109,47GE/mL plasma respectively. The lower ffDNA yield obtained using an automated DNA extraction procedure does not affect the efficiency of detecting fetal specific sequences in maternal plasma by rtPCR. Automated DNA extraction allows high throughput of samples (up to 72 samples/run) in a closed system thus greatly reducing the risk of cross contamination; it also requires less sample manipulation reducing overall costs and hands on time.
Prenatal and perinatal genetics P05.58 Partial submicroscopic duplications in markers D13s631 and X22 detected with QF PcR R. Raynova, S. Andonova, J. Genova, I. Kremensky; National Genetics Laboratory, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria. Rapid diagnosis by Quantitative Fluorescent PCR analysis (QF-PCR) has proved its cost-efficiency, speed and efficacy for prenatal detection of the most common autosome aneuploidies - trisomy 21, trisomy 18, trisomy 13. For the past three years in our laboratory QF-PCR was carried out on 2 300 prenatal samples (amniotic fluid, CVS). Fourteen polymorphic STR markers (4 located on chromosome 21, 4 - on chromosome 18, 3 - on chromosome 13, and 3 on chromosomes X and Y) were amplified with Cy5-labeled primers. Trisomy was indicated by at least two informative markers on a single chromosome, showing triallelic (1:1:1) or diallelic (1:2/2:1) trisomic pattern. In rare cases a single marker result, consistent with trisomy may be observed, whilst all other informative markers on the same chromosome are normal. A partial submicroscopic duplication could be suspected. We have found 9 samples to have a single marker result consistent with trisomy - 8 samples showed trisomic pattern for marker D13S631, one for marker X22. In cases when parental DNA was available we proved maternal or paternal origin of the duplication. Thus we could distinguish the rare inherited polymorphism from unbalanced translocation resulting to partial trisomy. P05.59 Large scale application of QF-PcR for rapid prenatal diagnosis of common chromosome aneuploidies, results of nine years clinical experience V. Cirigliano1 , G. Voglino2 , E. Ordoñez1 , P. Cañadas1 , L. Rueda1 , C. Fuster3 , M. Adinolfi4 ; 1 2 3 General Lab, Barcelona, Spain, Promea-Day Surgery, Turin, Italy, Universitat Autònoma de Barcelona, Barcelona, Spain, 4University College London, London, United Kingdom. Despite being deliberately targeted to chromosomes 13, 18, 21, X and Y the rapid QF-PCR test can detect the great majority of chromosome abnormalities in prenatal diagnosis. The main advantages of the assay are low cost, speed and automation allowing large scale application. We developed a QF-PCR assay that was employed to test 43.000 clinical samples with results issued in 24 hours. The most common referral indications were raised biochemical risk (32%) and advanced maternal age (30%). All samples were also tested by conventional cytogenetic analysis and the results compared. A total of 1550 non mosaic aneuploidies involving chromosomes 21, 18, 13 X and Y were detected with 100% specificity. Several cases of partial trisomies and mosaicism were also identified. Overall 95% of clinically relevant abnormalities were readily detected and termination of the affected pregnancies could be performed without waiting for results of the cytogenetic analyses.Our results support the possibility of reducing the load of prenatal cytogenetic tests if pregnancies are carefully monitored by non invasive screening. As a result, invasive procedures should only be performed in high risk pregnancies. In case of abnormal QF-PCR results, medical action can be made available in a few hours after sampling. In cases of negative QF-PCR results cytogenetic analyses might only be performed for fetuses with clear evidence of abnormalities based onl ultrasound results. In Countries, where large scale conventional cytogenetic tests are hampered by high cost and lack of technical expertise, QF-PCR may be used as the only prenatal diagnostic test P05.60 Rapid prenatal diagnosis by QF-PcR analysis on 700 cases A. M. Stan1 , C. Dragomir1 , E. Severin2 , L. Savu1 ; 1 2 Genetic Lab S.R.L., Bucharest, Romania, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania. The quantitative fluorescence PCR (QF-PCR) assay was recently introduced in Romania in the prenatal diagnosis field allowing the rapid detection of most frequent chromosomal aneuploidies involving chromosome 21, 18, 13, X and Y in high-risk pregnancies. The main objective of this study was to demonstrate that QF-PCR based assay is an efficient, reliable and rapid method that can reduce the number of conventional cytogenetic analysis in carefully monitored pregnancies. Therefore we performed rapid prenatal testing for 700 cases proceeding from small amounts of fetal sample including amniotic fluid, chorionic villi and products of conception. The methodology included the relative quantification of microsatellite alleles to determine sequence copy number, using a multiplex QF-PCR reaction and capillary electrophoresis. The multiplex QF-PCR reaction was performed with a commercial available kit for rapid prenatal diagnosis of trisomy 21, 18, 13 and sex chromosome aneuploidies. We analyzed 675 amniotic fluid samples, 13 products of conception and 12 chorionic villi samples. All samples with trisomy 21 (n=17), trisomy 18 (n=3), trisomy 13 (n=1), trisomy XXY (n=2), monosomy X (n=2), triploidy (n=2) and mosaicism (n=2) were accurately diagnosed without false-negative results. We detected somatic microsatellite mutation in two cases and submicroscopic polymorphic duplications in four samples, all six cases involving a single STR marker. All six cases were reported as normal by cytogenetic analysis. In conclusion we are confident that the QF-PCR approach is an efficient, reliable and rapid prenatal diagnosis method offering an alternative to conventional cytogenetic testing. P05.61 Analysis of heterozygosity level of stR markers by QF-PcR method for prenatal diagnostics in Northwest region of Russia I. Belotserkovsky, G. Demin, T. Ivashchenko, I. Fedorova, V. Baranov; Ott’s Institute of Obstetrics and Gynecology RAMS, Saint-Petersburg, Russian Federation. Last years prenatal diagnosis for the most common chromosome abnormalities, such as Down’s, Edward’s, Patau’s syndromes and also numerical sex chromosomes abnormalities has carried out by quantitative fluorescent PCR (QF-PCR). QF-PCR is highly sensitive and specific test revealing these chromosome abnormalities which account for around 95% of all chromosome pathologies of the fetus. We have used 11 chromosome-specific of markers (DXS6854, D13S628, D13S634, D13S742, D18S386, D18S380, D18S391, D18S535, D21S1270, D21S1411, D21S226) to determine the heterozygosity level for 203 DNA samples from Northwest region of Russia individuals. The lowest heterozygosity level was registered for D18S380 marker (59%) whereas the highest level was found 89% for D13S742 marker. The mean level of heterozygosity was found as 74%. When using two markers on the same chromosome heterozygosity level was increased: 99% - for chromosome 13; 91% - for chromosome 18 and 97% - for chromosome 21. Use of three and more markers on each chromosome increases level of heterozygosity and informativeness of the method up to 99-100%. Heterozygosity levels of D18S535 and D13S742 markers were significantly different from English population. We found that D13S742, D18S386 and D21S1411 markers are the most informative for prenatal diagnostics in Northwest region of Russia. P05.62 Quantitative real-time PcR technique for rapid and prenatal diagnosis of trisomy 21 syndrome A. R. Kamyab 1,2 , N. Masroori 2 , F. Maryami 1 , R. Mirfakhraie 3 , F. Maryami 1 , M. Karimipoor 1 , R. Mahdian 1 ; 1 Department of molecular medicine, Pasteur institute of Iran, Tehran, Islamic Republic of Iran, 2 Department of biology, science and research branch, Islamic Azad university, Tehran, Islamic Republic of Iran, 3 Department of medical genetics, National institute of genetic engineering and biotechnology, Tehran, Islamic Republic of Iran. Down’s syndrome (DS) is a genetic disorder that affects 1 in 700 live births across all ethnic groups. Trisomy 21 syndrome is caused by an extra copy of chromosome 21. Currently cytogenetic methods as karypotyping and FISH are used for diagnosis of DS. However these are labor and too time-consuming. On the contrary, molecular methods such as Real-Time PCR are sensitive and high throughput. According to the study, peripheral blood was collected from patient and normal controls. Subsequently by salting out method, genomic DNA was purified. In this study, two genes as DSCAM and DYRK1A2 (target genes) and PMP22 (reference gene) locating on chromosome 21 and 17 respectively, selected and measured copy number of them in trisomy 21 patients and normal individuals. Then, DSCAM/PMP22 and DYRK1A2/PMP22 ratio was calculated by 2 -ΔΔCt formula. The results of Real-Time PCR showed the ratio of 1.71±0.16 and 1.01±0.10 (p
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Volume 17 Supplement 2 May 2009 www
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European Society of Human Genetics
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Table of Contents spoken Presentati
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Plenary Lectures PL2.2 massive para
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Concurrent Symposia s01.1 Genome va
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Concurrent Symposia Monogenic diabe
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Concurrent Symposia invariable in t
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Concurrent Symposia s11.2 clinical,
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Concurrent Symposia s13.2 A novel g
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Concurrent Sessions c01.1 mRNA-seq
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Concurrent Sessions velopmental del
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Concurrent Sessions development of
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Concurrent Sessions c04.6 Duplicati
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Concurrent Sessions genes to be rec
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Concurrent Sessions c07.5 Prenatal
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Concurrent Sessions with familial h
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Concurrent Sessions University of W
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Concurrent Sessions with this, we f
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Concurrent Sessions had immotile ci
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Concurrent Sessions abnormal glycos
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Concurrent Sessions showers’ and
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Concurrent Sessions partial gene de
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Concurrent Sessions leads to distre
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Genetic counseling Genetics educati
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Clinical genetics and Dysmorphology
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Cytogenetics P03. cytogenetics Recu
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Cytogenetics use of metaphase analy
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Cytogenetics 2: mother’s age < fa
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Cytogenetics P03.028 HLA B27 allele
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Cytogenetics karyotype revealed a p
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Cytogenetics drome is estimated at
Page 117 and 118: Cytogenetics P03.057 Pathological c
Page 119 and 120: Cytogenetics grandmother and 2 mate
Page 121 and 122: Cytogenetics method used to detect
Page 123 and 124: Cytogenetics P03.082 High-resolutio
Page 125 and 126: Cytogenetics All detected anomalies
Page 127 and 128: Cytogenetics somy for chromosome 2.
Page 129 and 130: Cytogenetics cially in chromosome 4
Page 131 and 132: Cytogenetics (59.390.122 to 62.021.
Page 133 and 134: Cytogenetics For further characteri
Page 135 and 136: Cytogenetics 9p duplication. This c
Page 137 and 138: Cytogenetics regions with mental /d
Page 139 and 140: Cytogenetics donation program of po
Page 141 and 142: Cytogenetics P03.165 interpretation
Page 143 and 144: Cytogenetics P03.174 Deletion of th
Page 145 and 146: Cytogenetics P03.183 An atypical 7q
Page 147 and 148: Cytogenetics spermia, 11 oligosperm
Page 149 and 150: Reproductive genetics and social fa
Page 151 and 152: Reproductive genetics mosomal chang
Page 153 and 154: Reproductive genetics two cohorts w
Page 155 and 156: Reproductive genetics the 147 SC ch
Page 157 and 158: Prenatal and perinatal genetics P05
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Page 171 and 172: Cancer genetics P06.005 tiling reso
Page 173 and 174: Cancer genetics tient group in whic
Page 175 and 176: Cancer genetics chronic inflammatio
Page 177 and 178: Cancer genetics licular thyroid can
Page 179 and 180: Cancer genetics also studied. In 31
Page 181 and 182: Cancer genetics tile polyposis. We
Page 183 and 184: Cancer genetics Upon recombinant ex
Page 185 and 186: Cancer genetics variant allele was
Page 187 and 188: Cancer genetics from patients with
Page 189 and 190: Cancer genetics tion (PAX5 and GATA
Page 191 and 192: Cancer genetics scribed underexpres
Page 193 and 194: Cancer genetics of the ZIC gene fam
Page 195 and 196: Cancer genetics Materials and metho
Page 197 and 198: Cancer genetics the past and it is
Page 199 and 200: Cancer genetics P06.130 spectrum an
Page 201 and 202: Cancer genetics P06.139 the role of
Page 203 and 204: Cancer genetics and MSH2 germline m
Page 205 and 206: Cancer genetics P06.155 New roles f
Page 207 and 208: Cancer genetics screening was perfo
Page 209 and 210: Cancer genetics val (DFI) than pati
Page 211 and 212: Cancer genetics is hTERC gene ampli
Page 213 and 214: Cancer genetics on chromosome regio
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Cancer cytogenetics P07.08 molecula
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Statistical genetics, includes Mapp
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Complex traits and polygenic disord
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Evolutionary and population genetic
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Genomics, Genomic technology and Ep
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Molecular basis of Mendelian disord
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Metabolic disorders P12.167 Pattern
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Metabolic disorders PKU. BH4 challe
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Metabolic disorders catepe Universi
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Metabolic disorders respectively. G
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Metabolic disorders enzymaticaly co
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Metabolic disorders Normal Affected
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Therapy for genetic disorders in th
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Therapy for genetic disorders P14.0
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Therapy for genetic disorders of me
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Laboratory and quality management P
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Laboratory and quality management T
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Molecular and biochemical basis of
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Genetic analysis, linkage ans assoc
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Author Index Allanson, J.: P02.140
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Author Index 0 Barbacioru, C.: C01.
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Author Index 0 Bonneau, D.: C16.2,
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Author Index 0 Chakravarti, A.: C13
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Author Index 0 Dan, D.: P01.39, P14
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Author Index 0 Duskova, J.: P06.012
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Author Index Franke, A.: P09.056 Fr
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Author Index Grasso, R.: P02.025 Gr
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Author Index Holder-Espinasse, M.:
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Author Index Jurkiewicz, E.: C14.5
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Author Index Kooper, A. J. A.: P05.
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Author Index Li, K. J.: P11.086 Li,
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Author Index Martinet, D.: P03.095
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Author Index Moorman, A. F. M.: P16
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Author Index P10.57, P10.82 Oguzkan
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Author Index P09.054, P09.085, P09.
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Author Index P16.01 Renieri, A.: P0
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Author Index Santorelli, F.: P08.55
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Author Index Sinke, R. J.: P02.020
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Author Index Taheri, M.: P04.33, P0
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Author Index Valentino, P.: P02.064
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Author Index Wiemer-Kruel, A.: P14.
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Keyword Index 1 10q22 deletions: P0
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Keyword Index autosomal dominant re
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Keyword Index CLA: P06.073 CLCN1 ge
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Keyword Index DMD: P16.40, P16.41,
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Keyword Index gene networks: S12.2
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Keyword Index hydrocephaly: P05.11
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Keyword Index malignant hyperthermi
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Keyword Index NAT2: P12.118 natridi
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Keyword Index Polymalformations: P0
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Keyword Index Sardinia: C09.6 Sardi
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Keyword Index TNFalpha: P08.61, P09
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2009 Vienna - European Society of Human Genetics

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