Osteonecrosis of the Jaw After Bisphosphonates Treatment in Patients with Multiple Myeloma

Bone lytic lesion in Multiple myeloma are the most commonly presented symptoms which require treatment with bisphosphonates (BPs). BPs are providing supportive care, reducing the rate of skeletal morbidity but evidently not abolishing it, the criteria for stopping their administration have to be different from those used for classic antineoplastic drugs, and they should not be stopped when metastatic bone disease is progressing. Osteonecrosis of the jaw (ONJ) has been associated recently with the use of BPs. The aim of these study is to evaluate the incidence of ONJ in patients with MM treated with mixed biphosphonates. We analyzed total 296 myeloma patients (150 male and 146 female). Mostly effected age group with 58,1% is age more than 60 years up to 88 years, diagnosed in our institution in the period 2005-2015. We used intravenous or oral forms of biphosphonates such as pamidronate, ibandronate, clodronate and zolendronic acid. The patients were evaluated for ONJ. The incidence of ONJ in our group of patients treated with Bps was 4,6% from our group of 260 patients 87,8% received BPs therapy and patients which haven’t received BPs 12,2%. From this group, 95,4% (248) didn’t show ONJ, and 4,6% (12) showed ONJ. The period of this treatment with BPs is an important risk factor for development of ONJ, average duration of BPs therapy in patients which show adverse effects is 26.8±13.7 months, from the total number of 12 patients that developed ONJ adverse effects, we have 8 patients which received treatment with Zolendronic acid and the remaining 4 patients which were treated with other BPs combinations without Zolendronic acid. All patients treated for MM must continue with the therapy with Zolendronic acid and Pamidronate, each patient must be individually treated according to his response of the treatment (dose, frequency and duration of therapy)

Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach

Background A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets. Methods The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg. Results Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics. Data availability Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/

Population structure and genome characterization of local pig breeds in Russia, Belorussia, Kazakhstan and Ukraine

International audienceBackground It is generally accepted that domestication of pigs took place in multiple locations across Eurasia; the breeds that originated in Europe and Asia have been well studied. However, the genetic structure of pig breeds from Russia, Belorussia, Kazakhstan and Ukraine, which represent large geographical areas and diverse climatic zones in Eurasia, remains largely unknown.ResultsThis study provides the first genomic survey of 170 pigs representing 13 breeds from Russia, Belorussia, Kazakhstan and Ukraine; 288 pigs from six Chinese and seven European breeds were also included for comparison. Our findings show that the 13 novel breeds tested derived mainly from European pigs through the complex admixture of Large White, Landrace, Duroc, Hampshire and other breeds, and that they display no geographic structure based on genetic distance. We also found a considerable Asian contribution to the miniature Siberian pigs (Minisib breed) from Russia. Apart from the Minisib, Urzhum, Ukrainian Spotted Steppe and Ukrainian White Steppe breeds, which may have undergone intensive inbreeding, the breeds included in this study showed relatively high genetic diversity and low levels of homozygosity compared to the Chinese indigenous pig breeds.ConclusionsThis study provides the first genomic overview of the population structure and genetic diversity of 13 representative pig breeds from Russia, Belorussia, Kazakhstan and Ukraine; this information will be useful for the preservation and management of these breeds

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935–1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation

Genome-wide SNP data unveils the globalization of domesticated pigs

Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural rev‑
 olution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K
 genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing
 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and
 Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography,
 migration, and selection.Results: A deep phylogeographic division refects the dichotomy between early domestication centers. In the core
 Eastern and Western domestication regions, Chinese pigs show diferentiation between breeds due to geographic
 isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas,
 Africa, and Australia refects European expansion during the sixteenth to nineteenth centuries. Human-mediated
 introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth
 centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between
 populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20%
 of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate
 ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identifed highly diferentiated loci that
 include candidate genes related to muscle and body development, central nervous system, reproduction, and energy
 balance, which are putatively under artifcial selection.Conclusions: Key events related to domestication, dispersal, and mixing of pigs from diferent regions are refected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the
 past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and
 past selection, acting at diferent times and on diferent genetic backgrounds, enhance our insight in the mechanism
 of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agro‑
 diversity, but also provide a necessary framework for directing genetic conservation

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation

Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs

An amendment to this paper has been published and can be accessed via the original article

MOESM11 of Genome-wide SNP data unveils the globalization of domesticated pigs

Additional file 11: Figure S9. Distribution of haplotype diversity for pig populations across the world. Diamonds and vertical bars represent means and standard deviations of number of haplotypes respectively in 5-SNP s (A), 10-SNP (B), and 15-SNP (C) windows across the genome for each population with a minimum of 10 individuals

Description_data_GSE_Global_pigs

Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process