Stories and Challenges of Genome Wide Association Studies in Livestock — A Review

Aditi Sharma,Jun Seop Lee,Chang Gwon Dang,Pita Sudrajad,Hyeong Cheol Kim,Seong Heum Yeon,Hee Seol Kang,이승환 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.10

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

Clinical analysis of neck node metastasis in oral cavity cancer

Sharma, Aditi,Kim, Jin-Wook,Paeng, Jun-Young The Korean Association of Oral and Maxillofacial S 2018 대한구강악안면외과학회지 Vol.44 No.6

Objectives: The purpose of this study was to evaluate the neck node metastasis pattern and related clinical factors in oral cavity cancer patients. Materials and Methods: In total, 76 patients (47 males, 29 females) with oral squamous cell carcinoma (OSCC) who had no previous malignancies and were not undergoing neoadjuvant concomitant chemoradiotherapy or radiotherapy were selected for analysis. Results: Occult metastases were found in 8 of 52 patients with clinically negative nodes (cN0, 15.4%). Neck node metastases were found in 17 patients (22.4%). There was a statistically significant relationship between neck node metastasis and T stage (P=0.014) and between neck node metastasis and distant metastasis (Fisher's exact test, P=0.019). Conclusion: Neck node metastasis was significantly related to tumor size and distant metastasis during follow-up.

Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

Sharma, Aditi,Lim, Dajeong,Chai, Han-Ha,Choi, Bong-Hwan,Cho, Yongmin Korea Genome Organization 2016 Genomics & informatics Vol.14 No.4

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

The bovin phylogeny: A review

Sharma, Aditi,Lee, SeungHwan,Lee, JunHeon,Dang, Changgwon,Kim, Hyeong Cheul,Yeon, SeongHum,Kang, HeeSeol,Kanwar, Shamsher Singh,Vijh, Ramesh Kumar Institute of Agricultural Science 2014 Korean Journal of Agricultural Science Vol.41 No.4

The evolutionary history of cattle and buffalo has always been a topic of great interest to the evolutionary biologists. The phylogenetic studies of bovin species has been carried out at various levels, varying from the study of domestication and migration of populations to major cladogenesis. Along with the archeological studies there are studies from molecular biology and more recently from genomics. The phylogenetic perspective of the bovins and their evolutionary history, are reviewed in terms of what has been done, what needs to be done and potential challenges in doing it.

Stories and Challenges of Genome Wide Association Studies in Livestock - A Review

Sharma, Aditi,Lee, Jun Seop,Dang, Chang Gwon,Sudrajad, Pita,Kim, Hyeong Cheol,Yeon, Seong Heum,Kang, Hee Seol,Lee, Seung-Hwan Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.10

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Sharma, Aditi,Park, Jong-Eun,Park, Byungho,Park, Mi-Na,Roh, Seung-Hee,Jung, Woo-Young,Lee, Seung-Hwan,Chai, Han-Ha,Chang, Gul-Won,Cho, Yong-Min,Lim, Dajeong Korea Genome Organization 2018 Genomics & informatics Vol.16 No.1

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.

Clinical Characteristics of Postoperative Maxillary Cyst

Sharma, Aditi,Kim, Do-Hyung,Choi, So-Young,Kim, Jin-Wook,Kwon, Tae-Geon,Paeng, Jun-Young Korean Academy of Dental Science 2017 Journal of korean dental science Vol.10 No.2

Purpose: The purpose of this study is to analyze the clinical features of postoperative maxillary cyst (POMC) according to the patient's medical history of previous sinus operation and symptoms with radiological characteristics. Materials and Methods: The subjects of this study were 41 patients who had been diagnosed with POMC via clinical and histological examination from 2007 to 2016. Result: Thirty-five patients had medical histories of Caldwell-Luc procedures and four patients had maxillary sinus surgery, such as cyst enucleation and open reduction for maxillary bony fractures. From the computed tomography images, 25.6% (11/43) showed multilocular cysts and 74.4% (32/43) showed unilocular lesions. As for the treatment methods, cyst enucleation was conducted on 34 patients, and among them, three were treated previously with marsupialization. Their symptoms included diverse locations of pain and swelling. Conclusion: The clinical features of POMC varied from unilocular to multilocular and the symptoms included pain and swelling.

The bovin phylogeny

Aditi Sharma,SeungHwan Lee,JunHeon Lee,Changgwon Dang,Hyeong Cheul Kim,SeongHum Yeon 충남대학교 농업과학연구소 2014 농업과학연구 Vol.41 No.4

The evolutionary history of cattle and buffalo has always been a topic of great interest to the evolutionary biologists. The phylogenetic studies of bovin species has been carried out at various levels, varying from the study of domestication and migration of populations to major cladogenesis. Along with the archeological studies there are studies from molecular biology and more recently from genomics. The phylogenetic perspective of the bovins and their evolutionary history, are reviewed in terms of what has been done, what needs to be done and potential challenges in doing it.

Clinical Characteristics of Postoperative Maxillary Cyst

Aditi Sharma,김도형,최소영,김진욱,권태건,팽준영 대한치의학회 2017 Journal of korean dental science Vol.10 No.2

Purpose: The purpose of this study is to analyze the clinical features of postoperative maxillary cyst (POMC) according to the patient’s medical history of previous sinus operation and symptoms with radiological characteristics. Materials and Methods: The subjects of this study were 41 patients who had been diagnosed with POMC via clinical and histological examination from 2007 to 2016. Result: Thirty-five patients had medical histories of Caldwell-Luc procedures and four patients had maxillary sinus surgery, such as cyst enucleation and open reduction for maxillary bony fractures. From the computed tomography images, 25.6% (11/43) showed multilocular cysts and 74.4% (32/43) showed unilocular lesions. As for the treatment methods, cyst enucleation was conducted on 34 patients, and among them, three were treated previously with marsupialization. Their symptoms included diverse locations of pain and swelling. Conclusion: The clinical features of POMC varied from unilocular to multilocular and the symptoms included pain and swelling.

Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Aditi Sharma,박종은,박병호,박미나,노승희,정우영,이승환,최한하,조용민,임다정 한국유전체학회 2018 Genomics & informatics Vol.16 No.1

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.