• Title/Summary/Keyword: Genetic evaluation

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Evaluation of Gene Expression Changes of Serotonin Receptors, 5-HT3AR and 5-HT2AR as Main Stress Factors in Breast Cancer Patients

  • Hejazi, Seyed Hesam;Ahangari, Ghasem;Pornour, Majid;Deezagi, Abdolkhaleagh;Aminzadeh, Saeed;Ahmadkhaniha, Hamid Reza;Akbari, Mohamad Esmail
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.11
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    • pp.4455-4458
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    • 2014
  • Breast cancer is a serious and potentially lethal multi-factor disease among 40-50 aged women in both developed and developing countries. Also, various studies have pointed to roles of neurotransmitters like serotonin in development of cancers, through action on various types of receptors. This study was conducted to evaluate serotonin receptor (5HT2AR and 5HT3AR) genes expression in peripheral blood mononuclear cells (PBMCs) of breast cancer patients in comparison with the healthy people and in the MCF7 cell line. Peripheral blood samples were obtained from 30 patients and 30 healthy individuals. Total RNA was extracted from PBMCs and MCF-7 cells. and 5HT2AR and 5HT3AR were detected by RT-PCR techniques. Finally, serotonin receptor gene expression variation in breast cancer patients and MCF-7 cells were determined by real time-PCR. This latter indicated significant promotion in expression of 5HT3AR and 5HT2AR in PBMCs in breast cancer patients but expression of 5HT2AR in the MCF-7 cell line was significantly decreased. In conclusion, after performing complimentary tests, determine of gene expression changes in serotonin receptors (5HT2AR and 5HT3AR) may be useful as a new approach in treatment of breast cancer based on use of antagonists.

Partially Evaluated Genetic Algorithm based on Fuzzy Clustering (퍼지 클러스터링 기반의 국소평가 유전자 알고리즘)

  • Yoo Si-Ho;Cho Sung-Bae
    • Journal of KIISE:Software and Applications
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    • v.31 no.9
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    • pp.1246-1257
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    • 2004
  • To find an optimal solution with genetic algorithm, it is desirable to maintain the population sire as large as possible. In some cases, however, the cost to evaluate each individual is relatively high and it is difficult to maintain large population. To solve this problem we propose a novel genetic algorithm based on fuzzy clustering, which considerably reduces evaluation number without any significant loss of its performance by evaluating only one representative for each cluster. The fitness values of other individuals are estimated from the representative fitness values indirectly. We have used fuzzy c-means algorithm and distributed the fitness using membership matrix, since it is hard to distribute precise fitness values by hard clustering method to individuals which belong to multiple groups. Nine benchmark functions have been investigated and the results are compared to six hard clustering algorithms with Euclidean distance and Pearson correlation coefficients as fitness distribution method.

Strategies to Multiply Elite Cow in Hanwoo Small Farm

  • Lee, Seung Hwan;Kim, Ui Hyung;Dang, Chang Gwan;Aditi, Sharma;Kim, Hyeong Cheul;Yeon, Seung Heum;Jeon, Gi Jun;Chang, Sun Sik;Oh, Sung Jong;Lee, Hak Kyo;Yang, Bo Suk;Kang, Hee Seol
    • Journal of Embryo Transfer
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    • v.28 no.2
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    • pp.79-85
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    • 2013
  • The recent development in genetic assisted selection (combining traditional- and genome assisted selection method) and reproduction technologies will allow multiplying elite cow in Hanwoo small farm. This review describes the new context and corresponding needs for genome assisted selection schemes and how reproductive technologies can be incorporated to get more genetic gain for cow genetic improvement in Hanwoo. New improved massive phenotypes and pedigree information are being generated from commercial farm sector and these are allowing to do genetic evaluation using BLUP to get elite cows in Korea. Moreover cattle genome information can now be incorporated into breeding program. In this context, this review will discuss about combining the reproductive techniques (Multiple Ovulation Embryo Transfer; MOET) and genome assisted selection method to get more genetic gain in Hanwoo breeding program. Finally, how these technologies can be used for multiplication of elite cow in small farm was discussed.

Genetic Evaluation of First Lactation Traits in Sahiwal Cattle Using Restricted Maximum Likelihood Technique

  • Choudhary, V.;Kothekar, M.D.;Raheja, K.L.;Kasturiwale, N.N.;Khire, D.W.;Kumar, P.
    • Asian-Australasian Journal of Animal Sciences
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    • v.16 no.5
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    • pp.639-643
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    • 2003
  • The data on 283 Sahiwal cows, sired by 16 bulls, maintained at Cattle Breeding Farm of Nagpur Veterinary College and Dairy Farm of Agricultural College, Nagpur, were considered for the estimation of genetic parameters. Variance and covariance estimates of first lactation traits were obtained using restricted maximum likelihood technique (REML). When first lactation milk yield (FLMY), first lactation length (FLL) and average daily yield (ADY) traits were considered for REML analysis, the heritabilities were $0.184{\pm}0.146$, $0.132{\pm}0.131$ and $0.141{\pm}0.133$, respectively. While, genetic and phenotypic correlations between them were medium to high except phenotypic correlations between FLL and ADY (-0.025). REML procedure considering FLMY, age at first calving (AFC) and first service period (FSP) combination exhibits heritabilities as $0.274{\pm}0.173$, $0.506{\pm}0.233$ and $0.274{\pm}0.172$, respectively. Genetic correlations were $-0.120{\pm}0.376$, $0.225{\pm}0.423$ and $0.365{\pm}0.331$ between FLMY and AFC, FLMY and FSP, AFC and FSP, respectively. Phenotypic correlations were 0.057, 0.289 and 0.123, respectively. Considering all five traits REML combination heritabilities estimated were $0.238{\pm}0.162$, $0.160{\pm}0.139$, $0.136{\pm}0.132$, $0.409{\pm}0.209$ and $0.259{\pm}0.168$ for FLMY, FLL, ADY, AFC and FSP, respectively. The genetic correlations were positive except FLMY and AFC. The phenotypic correlations were also positive except FLL and ADY, ADY and FSP. Almost all estimates were associated with high standard error.

Cytogenetic and Genetic Mutation Features of de novo Acute Myeloid Leukemia in Elderly Chinese Patients

  • Su, Long;Li, Xian;Gao, Su-Jun;Yu, Ping;Liu, Xiao-Liang;Tan, Ye-Hui;Liu, Ying-Min
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.2
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    • pp.895-898
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    • 2014
  • Objectives: The present study aimed to examine the cytogenetic and genetic mutation features of acute myeloid leukemia (AML) in elderly Chinese patients. Methods: A retrospective analysis of cytogenetics and genetic mutations was performed in 113 cases (age range 50-82 years) with de novo AML. Results: The most frequent cytogenetic abnormality was t (15;17) (q22;q21), detected in 10.0% (n = 9) of successfully analyzed cases, followed by t (8;21) (q22;q22) in 8.89% (n = 8), and complex karyotypes in 5.56% (n = 5). Those with complex karyotypes included 4 cases (4.44%) of monosomal karyotypes. The frequencies of NPM1, FLT3-ITD, c-kit, and CEBPA mutations were 27.4% (31/113), 14.5% (16/110), 5.88% (6/102), and 23.3% (7/30), respectively. The complete remission rates of patients in low, intermediate, and high risk groups were 37.5%, 48.6%, and 33.3%, respectively (${\chi}^2$ = 0.704, P = 0.703) based on risk stratification. Conclusion: Cytogenetics and genetic mutations alone may not be sufficient to evaluate the prognoses of elderly AML patients. The search for a novel model that would enable a more comprehensive evaluation of this population is therefore imperative.

Optimum Design of Greenhouse Structures Using Genetic Algorithms (유전자알고리즘에 의한 온실구조의 최적설계)

  • Park, Choon Wook;Yuh, Baeg Youh;Lee, Hyun Woo;Lee, Suk Gun
    • Journal of Korean Society of Steel Construction
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    • v.19 no.2
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    • pp.171-179
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    • 2007
  • The greenhouse discrete optimum design program was developed using discrete optimum algorithm based on the genetic algorithm. The basic search method for the optimum design is the genetic algorithm, which is known to be very efficient for discrete optimization. In this paper, the objective function was the weight of the greenhouse structures and the constraints were the limits state design method. The design variables were galvanized steel pipes for plastic housing KSD 3760. Objective criteria were presented for the design of economic greenhouse structure and evaluation of its stability. The standardizations of greenhouse structure were used, as well as the normalization of greenhouse-related materials. Design examples were given to show the applicability of the optimum design using the discrete optimum algorithm based on the genetic algorithm of this study.

Prospective evaluation of the clinical utility of whole-exome sequencing using buccal swabbing for undiagnosed rare diseases

  • Chong Kun Cheon;Yong Beom Shin;Soo-Yeon Kim;Go Hun Seo;Hane Lee;Changwon Keum;Seung Hwan Oh
    • Journal of Genetic Medicine
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    • v.19 no.2
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    • pp.76-84
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    • 2022
  • Purpose: Whole-exome sequencing (WES) has been a useful tool for novel gene discovery of various disease categories, further increasing the diagnostic yield. This study aimed to investigate the clinical utility of WES prospectively in undiagnosed genetic diseases. Materials and Methods: WES tests were performed on 110 patients (age range, 0-28 years) with suspected rare genetic diseases. WES tests were performed at a single reference laboratory and the variants reported were reviewed by clinical geneticists, pediatricians, neurologists, and laboratory physicians. Results: The patients' symptoms varied with abnormalities in the head or neck, including facial dysmorphism, being the most common, identified in 85.4% of patients, followed by abnormalities in the nervous system (83.6%). The average number of systems manifesting phenotypic abnormalities per patient was 3.9±1.7. The age at presentation was 2.1±2.7 years old (range, 0-15 years), and the age at WES testing was 6.7±5.3 years (range, 0-28 years). In total, WES test reported 100 pathogenic/likely pathogenic variants or variants of uncertain significance for 79 out of 110 probands (71.8%). Of the 79 patients with positive or inconclusive calls, 55 (50.0%) patients were determined to have good genotype-phenotype correlations after careful review. Further clinical reassessment and family member testing determined 45 (40.9%) patients to have been identified with a molecular diagnosis. Conclusion: This study showed a 40.9% diagnostic yield for WES test for a heterogeneous patient cohort with suspected rare genetic diseases. WES could be the feasible genetic test modality to overcome the diversity and complexity of rare disease diagnostics.

Evaluation of models for estimation of genetic parameters for post-weaning body measurements and their association with yearling weight in Nellore sheep

  • Satish Kumar Illa;Gangaraju Gollamoori;Sapna Nath
    • Animal Bioscience
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    • v.37 no.3
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    • pp.419-427
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    • 2024
  • Objective: The objective of this study was to obtain (co) variance components and genetic parameter estimates for post-weaning body measurements such as body length (BL), height at withers (HW), and chest girth (HG) recorded at six (SBL, SHW, and SHG), nine (NBL, NHW, and NHG) and twelve (YBL, YHW, and YHG) months of age along with yearling weight (YW) in Nellore sheep maintained at livestock research station, Palamaner, Andhra Pradesh, India and also the association among body measurements with YW was studied. Methods: Data on 2,076 Nellore sheep (descended from 75 sires and 522 dams) recorded between 2007 and 2016 (10 years) were utilized in the study. Lambing year, sex of lamb, season of lambing and parity of dam were included in the model as fixed effects and ewe weight was kept as a covariate. Analyses were conducted with six animal models with different combinations of direct and maternal genetic effects using restricted maximum likelihood procedure. Best model for each trait was determined based on Akaike's information criterion. Results: Moderate estimates of direct heritability were obtained for the studied traits viz., BL (0.02 to 0.24), HW (0.31 to 0.49), and CG (0.08 to 0.35) and their corresponding maternal heritability estimates were in the range of 0.00 to 0.07 (BL), 0.13 to 0.17 (HW), and 0.07 to 0.13 (CG), respectively. Positive direct genetic and phenotypic correlations among the traits and they ranged from 0.07 (YBL-YW) to 0.99 (SBL-SHG, SHG-YW, and NBL-YBL) and 0.01 (SBL-YBL) to 0.99 (NBL-NHG), respectively. Further, the genetic correlations among all the body measurements and YW were positive and ranged from 0.07 (YW and YBL) to 0.99 (YW and SHG). Conclusion: There was a strong association of chest girth at six months with YW. Further, it is indicated that moderate improvement of post-weaning body measurements in Nellore sheep would be possible through selection.

National Genetic Evaluation (System) of Hanwoo (Korean Native Cattle)

  • Park, B.;Choi, T.;Kim, S.;Oh, S.H.
    • Asian-Australasian Journal of Animal Sciences
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    • v.26 no.2
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    • pp.151-156
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    • 2013
  • Hanwoo (Also known as Korean native cattle; Bos taurus coreanae) have been used for transportation and farming for a long time in South Korea. It has been about 30 yrs since Hanwoo improvement began in earnest as beef cattle for meat yield. The purpose of this study was to determine the trend of improvement as well as to estimate genetic parameters of the traits being used for seedstock selection based on the data collected from the past. Hanwoo proven bulls in South Korea are currently selected through performance and progeny tests. National Hanwoo genetic evaluations are implemented with yearling weight (YW), carcass weight (CW), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS). Yearling weights and MS are used for selecting young bulls, and EMA, BF, and MS are used for selecting proven bulls. One individual per testing room was used for performance tests, and five individuals per room for progeny tests. Individuals tested were not allowed to graze pasture, but there was enough space for them to move around in the testing room. Feeds including roughages and minerals were fed ad libitum, and concentrates were provided at the rate of about 1.8% of individual weight. Overall means of the traits were $352.8{\pm}38.56$ kg, $335.09{\pm}44.61$ kg, $77.85{\pm}8.838\;cm^2$, $8.6{\pm}3.7$ mm and $3.293{\pm}1.648$ for YW, CW, EMA, BF and MS. Heritabilities estimated in this study were 0.30, 0.30, 0.42, 0.50 and 0.63 in YW, CW, EMA, BF and MS, respectively, which are similar to results from previous research. Yearling weight was 315.54 kg in 1998, and had increased to 355.06 kg in 2011, resulting in about 40 kg of improvement over 13 yrs. YW and CW have improved remarkably over the past 15 yrs. Breeding values between 1996 and 2000 decreased or did not change much, but have moved in a desirable direction since 2001. These improvements correspond with the substantial increase in use of animal models since the late 1990s in Korea. Hanwoo testing programs have practically contributed to the improvement in aspects of quality and quantity. In sum, the current selection system is good enough to accommodate circumstances where fewer sires are used on many more cows. Although progeny tests take longer and cost more, they seem to be appropriate under the circumstances of the domestic market with its higher requirement for better meat quality. Consequently, accumulative data collection, genetic evaluation model development, revision of selection indices, as well as cooperation among farms, associations, National Agricultural Cooperative Federation, universities, research institutes, and government agencies must be applied to the Hanwoo selection program. All these efforts will assist the domestic market to secure a competitive position against imported beef under Free Trade Agreement trade system and will provide farmers with higher profits as well as the public with a higher quality of beef.

XRCC1 Gene Polymorphisms and Breast Cancer Risk: A Systematic Review and Meta-analysis Study

  • Moghaddam, Ali Sanjari;Nazarzadeh, Milad;Moghaddam, Hossein Sanjari;Bidel, Zeinab;Karamatinia, Aliasghar;Darvish, Hossein;Jarrahi, Alireza Mosavi
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.sup3
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    • pp.323-335
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    • 2016
  • Breast cancer risk assessment has developed during years and evaluation of genetic factor affecting risk of breast cancer is an important component of this risk assessment. The aim of this meta-analysis was to investigate the role of XRCC1 polymorphisms (Arg194Trp, Arg280His and Arg399Gln) in risk of breast cancer among different population and categories of menopausal status.PubMed, Medline, Web of Science, and PubMed Central were systematically searched to identify studies evaluating association between breast cancer and XRCC1 gene polymorphisms (Arg194Trp, Arg280His and Arg399Gln). Two authors independently extracted required information. Odds Ratios were pooled for four genetic inheritance models using both fixed and the DerSimonian and Laird random-effect models. Egger's test and contour-enhanced funnel plot was used to evaluate publication bias and small study effect. Additional subgroup analysis was performed for menopausal status, ethnicity, and source of controls. After evaluation and applying inclusion criteria on extracted studies, fifty three studies were included in this meta-analysis. For polymorphisms of Arg194Trp and Arg280His, no significant association was observed in all genetic models. Arg194Trp had a protective effect in post-menopausal status only in homozygote model (OR=0.57 [0.37-0.88]). Arg399Gln showed significant association with breast cancer in homozygote (OR=1.21 [1.10-1.34]), dominant (OR=1.09 [1.03-1.15]) and recessive (OR=1.21 [1.09- 1.35]) genetic models. Arg399Gln was associated with higher risk in post-menopausal status for homozygote and heterozygote models. Our findings suggest that XRCC1 gene polymorphisms modify breast cancer risk in different populations and different categories of menopausal status.