ASSESSMENT OF RECENT INBREEDING OF THE HOLSTEINIZED CATTLE

2020 ◽  
Author(s):  
М.Г. СМАРАГДОВ
Keyword(s):  
Quality Control ◽  
Animal Husbandry ◽  
Inbreeding Coefficient ◽  
Leningrad Region ◽  
Science Center ◽  
Heterozygous Snps ◽  
Total Size ◽  
Russian Research Institute ◽  
The Mean ◽  
Breeding Farms

Изучено влияние неучтенных гетерозиготных и негенотипированных SNPs в протяженных гомозиготных сегментах (ROH) на среднее количество и средний суммарный размер ROH-сегментов, а также на вычисление коэффициента инбридинга у голштинизированных черно-пестрых коров. Из 6 племенных заводов Ленинградской области были отобраны 374 коровы. Полногеномное генотипирование их осуществляли чипом BovineSNP50 v2. При выполнении контроля качества однонуклеотидного полиморфизма (SNP) генотипов коров и полногеномном сканировании ROH использовали программу Plink 1.9. После проведения контроля качества SNP-генотипов из 54609 осталось 43298 SNPs. Влияние неучтенных гетерозиготных и негенотипированных SNPs на результаты ROH сканирования оценивали при изменении этих показателей от 0 до 16. Оказалось, что негенотипированные SNPs не влияли на показатели ROH, тогда как количество неучтенных гетерозиготных SNPs существенно влияло на результаты ROH сканирования. Так, по мере увеличения количества неучтенных гетерозиготных SNPs в ROH-сегментах среднее количество ROH-сегментов и их средний суммарный размер в геноме коров росли экспоненциально. При этом средний размер ROH-сегментов в геноме коров менялся незначительно 10,4±1,2 Mb. В зависимость от количества гетерозиготных SNPs коэффициент инбридинга также рос экспоненциально. В случае отсутствия гетерозиготных SNPs в ROH-сегментах средний коэффициент инбридинга у коров в 6 стадах изменялся от 4,4±0,4 до 5,6±0,2. Предполагается, что полученные результаты обусловлены не случайным расположением ROH-сегментов, а их кластеризацией в хромосомах коров. Таким образом, для несмещенной оценки результатов ROH-анализа следует исключать гетерозиготные SNPs в ROH-сегментах. Russian Research Institute of Farm Animal Genetics and Breeding Branch of the L.K. Ernst Federal Science Center for Animal Husbandry The aim of this study was to assess the effect of non-genotyped and heterozygous SNPs in ROH segments at the average number and average total size of ROH segments, as well as at the calculation of the inbreeding coefficient of Holsteinized Back-and-White cows. Of the six breeding farms in the Leningrad Region, 374 cows were selected. Whole — genome genotyping was carried out with the BovineSNP50 v2 chip. When performing quality control of the genotyped cows and genome-wide ROH runs, the Plink 1.9 program was used. Upon quality control of the SNP genotypes out of 54609, 43298 SNPs were remained. The effect of non-genotyped and heterozygous SNPs at the results of ROH runs was evaluated by changing these parameters from 0 to 16. It turned out that non-genotyped SNPs did not affect the ROH scores, while the number of allowed heterozygous SNPs significantly affected the results of ROH runs. Thus, as the number of allowed heterozygous SNPs in ROH segments were increased, the mean number of ROH segments and their mean total size in the cows’ genome increased exponentially. Nevertheless, the mean size of the ROH segment changed slightly 10.4±1.2 Mb. Depending on the number of heterozygous SNPs in ROH, the inbreeding coefficient as well increased exponentially. In the absence of heterozygous SNPs in ROH segments, the average inbreeding coefficient of the cows in six herds varied from 4.4±0.4 to 5.6±0.2. It is suggested that obtained results are not due to the random distribution of ROH segments, but their clustering in the chromosomes of the cows. Thus, for unbiased assessment of the results of ROH analysis, heterozygous SNPs in ROH segments should be excluded.

scholarly journals PSVII-29 Genetic differentiation of modern and historical samples of the Russian Large White pigs

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 466-466
Author(s):  
Olga V Kostyunina ◽  
Lyubov Getmantseva ◽  
Alexandra Abdelmanova ◽  
Lidia Petrikeeva ◽  
Natalia A Zinovieva
Keyword(s):  
Quality Control ◽  
Molecular Genetic ◽  
Research Result ◽  
Animal Husbandry ◽  
Fixation Index ◽  
Science Center ◽  
Large White ◽  
Bone Powder ◽  
Thermo Fisher Scientific ◽  
Historical Samples

Abstract Involvement in research of historical samples can help to clarify the demographic processes in livestock populations. In most cases, bone powder derived from teeth or skull bones are used for molecular genetic studies of historical samples. The aim of our study was to evaluate genetic differences between historical and modern samples of the Russian Large White pigs. Eight historical specimens of the Large White pigs dated by 60s of the 20th century which are maintained in the Craniological collection of the Livestock Museum named after E.F. Liskun were used for the study. The modern representatives of breed were presented by the samples from eight different farms (LW_New1 - LW_New8, n = 152). All works with historical DNA were carried out in the special facilities of the L.K. Ernst Federal Science Center for Animal Husbandry dedicated for work with ancient DNA. DNA was isolated using COrDIS “Extract” Decalcin kit (COrDIS, Russia) and Prep Filer™ BTA Forensic DNA Extraction Kit (Thermo Fisher Scientific, USA). The whole-genome genotyping was performed using Porcine GGP HD BeadChip chips (Illumina/Novogene, USA). The quality control was performed in PLINK 1.9 using the following settings: geno-0.2, mind-0.2, MAF-0.01, HWE-P< 8.27×10−7. The fixation index (Fst) was calculated using the ADMIXTURE software. The concentration of DNA isolated from the historical samples was varied from 0.550 to 600 ng/μl (A260/280 = 1.46–1.96). The genotypes’ call rates were 0.187–0.986. Six historical samples passed through the quality control were used for the further study. Calculation of Fst values showed, that the historical samples were closer to the LW_new1 and LW_new4 groups (Fst = 0.151 and 0.157, respectively), and the most divergent from the LW_new3 group (Fst = 0.304). Our research result will help to elucidate the genetic architecture of the Russian Large White pigs. This research was supported by the RSF (Project No. 19-16-00109).

scholarly journals Daily Quality Control in CD3+and CD4+T Cell Estimation by the FACSCount System at a Tertiary Care Center in South India

2012 ◽  
Vol 19 (10) ◽  
pp. 1693-1696 ◽  
Author(s):  
Veena V. Ramalingam ◽  
Monika Mani ◽  
Vijayanand C. Sundaresan ◽  
Ramesh J. Karunaiya ◽  
Jaiprasath Sachithanandham ◽  
...  
Keyword(s):  
Quality Control ◽  
T Cell ◽  
South India ◽  
Care Center ◽  
Tertiary Care ◽  
Cd4 T Cell ◽  
Internal Quality ◽  
Cell Counts ◽  
Resource Poor ◽  
The Mean

ABSTRACTCD4+T cell count estimations are subject to high variations; hence, in this study, the previous day's tested samples were included routinely as the internal quality controls. The percentages of variation of the 2-day values were analyzed for 280 observations and the mean variation for CD4+and CD3+T cell counts ranged from 5.21% to 9.66%. This method is a good internal quality control (IQC) procedure for the estimation of CD3+and CD4+T cell counts in resource-poor settings.

scholarly journals Overview of large building testing in Baltic countries

2020 ◽  
Vol 172 ◽  
pp. 05007
Author(s):  
Andrejs Nitijevskis ◽  
Vladislavs Keviss
Keyword(s):  
Quality Control ◽  
Pressure Difference ◽  
Leakage Rate ◽  
Air Leakage ◽  
Baltic Countries ◽  
Measurement Results ◽  
The Mean ◽  
Mandatory Testing ◽  
Air Leakage Rate ◽  
Large Building

The objectives of this paper are to review measurements of airtightness of 2 large building groups – middle size shops, and warehouses/distribution centres. The mean air leakage rate at 50 Pa pressure difference q50 was 1.04 m3/m2h and 1.35 m3/m2h for shops and warehouses respectively. Analysis of measurement results is valuable because it allows to make a conclusion about compliance of national and corporative construction airtightness norms with actual air barrier condition on a comissioning stage. In the concluding part of the study there are suggested ways to improve air barrier such as review of construction norms, implementation of a mandatory testing and quality control of a measurement.

scholarly journals Internal quality control in blood and component bank in a tertiary healthcare center in Northern India

2021 ◽  
Vol 6 (2) ◽  
pp. 115-118
Author(s):  
Kafil Akhtar ◽  
Radhika Arora ◽  
Umrah Malik ◽  
Ankita Parashar ◽  
Murad Ahmad ◽  
...  
Keyword(s):  
Quality Control ◽  
Factor Viii ◽  
Red Cells ◽  
Internal Quality Control ◽  
Internal Quality ◽  
Blood Component ◽  
Minimal Risk ◽  
Blood Components ◽  
The Mean ◽  
Rbc Count

Quality control describes steps taken by blood and component bank to ensure that tests are performed correctly. Primary goal of quality control is transfusion of safe quality of blood. It is to ensure availability of efficient supply of blood and blood components. Internal quality control is the backbone of quality assurance program. To analyze the internal quality control of blood components in modern blood banking as an indicator of our blood bank performance. An observational cross sectional study conducted at the Blood and Component Bank, JN Medical College and Hospital from 2018 to 2020. Each blood component was arbitrarily chosen during the study on monthly basis. Selection criteria was 1.0% of total collection or minimum 4 bags per month. Packed red cells were evaluated for hemoglobin, hematocrit, RBC count; platelet concentrates for pH, yield and culture; fresh frozen plasma and cryoprecipitate were evaluated for unit volume, factor VIII and fibrinogen concentration. The mean HCT of packed red cells was 65.75+7.42%, volume was 238+26.25ml, Hb was 20.5+0.15g/dL and RBC count of 5.89x10+0.30x10. The mean platelet yield was 5.7x10, pH was ≥6.8+0.175 and volume was 82.5+13.75ml; cultures were negative and swirling was present in all the platelet units tested. Mean factor VIII and fibrinogen levels were found to be 95.25 +7.37and 307.5+41.37gm/l for FFP respectively. Mean volume, PT and APTT were 215+32.5ml, 14.15+0.325 sec and 29.50+1.5 sec respectively. The quality control of blood components ensures the timely availability of a blood component of high quality with maximum efficacy and minimal risk to potential recipients.

scholarly journals IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽  
1977 ◽  
Vol 86 (3) ◽  
pp. 697-713
Author(s):  
C Chevalet ◽  
M Gillois ◽  
R F Nassar
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Random Mating ◽  
Matrix Multiplication ◽  
Inbred Lines ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Mean ◽  
Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

scholarly journals Implementation of a Blind Quality Control Program in Blood Alcohol Analysis

2019 ◽  
Vol 43 (8) ◽  
pp. 630-636 ◽  
Author(s):  
Jackeline Moral ◽  
Callan Hundl ◽  
Dayong Lee ◽  
Maddisen Neuman ◽  
Aimee Grimaldi ◽  
...  
Keyword(s):  
Quality Control ◽  
Linear Regression Analysis ◽  
Control Program ◽  
Multiple Linear Regression Analysis ◽  
Blood Alcohol ◽  
Proficiency Tests ◽  
Science Center ◽  
Quality Control Program ◽  
Significant Difference ◽  
The Difference

Abstract Declared proficiency tests are limited in their use for testing the performance of the entire system, because analysts are aware that they are being tested. A blind quality control (BQC) is intended to appear as a real case to the analyst to remove any intentional or subconscious bias. A BQC program allows a real-time assessment of the laboratory’s policies and procedures and monitors reliability of casework. In September 2015, the Houston Forensic Science Center (HFSC) began a BQC program in blood alcohol analysis. Between September 2015 and July 2018, HFSC submitted 317 blind cases: 89 negative samples and 228 positive samples at five target concentrations (0.08, 0.15, 0.16, 0.20 and 0.25 g/100 mL; theoretical targets). These blood samples were analyzed by a headspace gas chromatograph interfaced with dual-flame ionization detectors (HS-GC-FID). All negative samples produced `no ethanol detected’ results. The mean (range) of reported blood alcohol concentrations (BACs) for the aforementioned target concentrations was 0.075 (0.073–0.078), 0.144 (0.140–0.148), 0.157 (0.155–0.160), 0.195 (0.192–0.200) and 0.249 (0.242–0.258) g/100 mL, respectively. The average BAC percent differences from the target for the positive blind cases ranged from −0.4 to −6.3%, within our uncertainty of measurement (8.95–9.18%). The rate of alcohol evaporation/degradation was determined negligible. A multiple linear regression analysis was performed to compare the % difference in BAC among five target concentrations, eight analysts, three HS-GC-FID instruments and two pipettes. The variables other than target concentrations showed no significant difference (P > 0.2). While the 0.08 g/100 mL target showed a significantly larger % difference than higher target concentrations (0.15–0.25 g/100 mL), the % differences among the higher targets were not concentration-dependent. Despite difficulties like gaining buy-in from stakeholders and mimicking evidence samples, the implementation of a BQC program has improved processes, shown methods are reliable and added confidence to staff’s testimony in court.

scholarly journals The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 498 ◽  
Author(s):  
Antonio Boccardo ◽  
Stefano Paolo Marelli ◽  
Davide Pravettoni ◽  
Alessandro Bagnato ◽  
Giuseppe Achille Busca ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Inbreeding Coefficient ◽  
Nucleotide Polymorphisms ◽  
Canis Lupus Familiaris ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
The Mean ◽  
Dog Breed ◽  
Genomic Inbreeding ◽  
Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

scholarly journals Impact of Variability in Portal Venous Phase Acquisition Timing in Tumor Density Measurement and Treatment Response Assessment: Metastatic Colorectal Cancer as a Paradigm

2017 ◽  
pp. 1-8 ◽  
Author(s):  
Laurent Dercle ◽  
Lin Lu ◽  
Philip Lichtenstein ◽  
Hao Yang ◽  
Deling Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Quality Control ◽  
Metastatic Colorectal Cancer ◽  
Imaging Biomarkers ◽  
Portal Venous Phase ◽  
Computed Tomography Images ◽  
Choi Criteria ◽  
Computer Aided ◽  
Venous Phase ◽  
The Mean

Purpose New response patterns to anticancer drugs have led tumor size–based response criteria to shift to also include density measurements. Choi criteria, for instance, categorize antiangiogenic therapy response as a decrease in tumor density > 15% at the portal venous phase (PVP). We studied the effect that PVP timing has on measurement of the density of liver metastases (LM) from colorectal cancer (CRC). Methods Pretreatment PVP computed tomography images from 291 patients with LM-CRC from the CRYSTAL trial (Cetuximab Combined With Irinotecan in First-Line Therapy for Metastatic Colorectal Cancer; ClinicalTrials.gov identifier: NCT00154102) were included. Four radiologists independently scored the scans’ timing according to a three-point scoring system: early, optimal, late PVP. Using this, we developed, by machine learning, a proprietary computer-aided quality-control algorithm to grade PVP timing. The reference standard was a computer-refined consensus. For each patient, we contoured target liver lesions and calculated their mean density. Results Contrast-product administration data were not recorded in the digital imaging and communications in medicine headers for injection volume (94%), type (93%), and route (76%). The PVP timing was early, optimal, and late in 52, 194, and 45 patients, respectively. The mean (95% CI) accuracy of the radiologists for detection of optimal PVP timing was 81.7% (78.3 to 85.2) and was outperformed by the 88.6% (84.8 to 92.4) computer accuracy. The mean ± standard deviation of LM-CRC density was 68 ± 15 Hounsfield units (HU) overall and 59.5 ± 14.9 HU, 71.4 ± 14.1 HU, 62.4 ± 12.5 HU at early, optimal, and late PVP timing, respectively. LM-CRC density was thus decreased at nonoptimal PVP timing by 14.8%: 16.7% at early PVP ( P < .001) and 12.6% at late PVP ( P < .001). Conclusion Nonoptimal PVP timing should be identified because it significantly decreased tumor density by 14.8%. Our computer-aided quality-control system outperformed the accuracy, reproducibility, and speed of radiologists’ visual scoring. PVP-timing scoring could improve the extraction of tumor quantitative imaging biomarkers and the monitoring of anticancer therapy efficacy at the patient and clinical trial levels.

Use of the Reference Method for Determination of Serum Calcium in a Quality-Assurance Survey

1975 ◽  
Vol 21 (10) ◽  
pp. 1416-1421 ◽  
Author(s):  
John F Pickup ◽  
Malcolm J Jackson ◽  
E Margaret Price ◽  
Michael J R Healy ◽  
Stanley S Brown
Keyword(s):  
Quality Control ◽  
Continuous Flow ◽  
Reference Method ◽  
Control Programme ◽  
Total Calcium ◽  
Small Constant ◽  
Constant Bias ◽  
The Mean ◽  
Quality Control Programme

Abstract The Reference Method [Clin. Chem. 19, 1208 (1973)] for determination of total calcium in serum has been applied to 29 specimens from the Wellcome Group Quality-Control Programme. The accuracy of the mean resuIts for all participants, and for selected groups of participants, was determined over the concentration range 2.00-2.75 mmol/liter. We show that, in general, continuous-flow (AutoAnalyzer) and atomic absorption methods of analysis have a small, constant bias, but chelation (ethylenediaminetetraacetate) methods are unpredictably inaccurate.

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