Breeding and Economic Aspects of Cytogenetic Screening Studies of Pigs Qualified for Reproduction

Cytogenetic monitoring allows the identification and early removal of pigs affected by inherited karyotype defects from breeding herds. These abnormalities cause developmental anomalies, considerably reducing the fertility (by several dozen to 100%) and performance parameters of breeding herds, resulting in substantial financial losses. This mainly concerns reciprocal translocations, typical of pigs, which are highly prevalent (about 0.46%), generally occur de novo, and normally result in low breeding soundness of the carriers. Due to the potential spontaneous occurrence of chromosomal aberrations and the rapid spread of these genetic defects in the population, especially under artificial insemination conditions, it is necessary to perform routine karyotype screening of animals qualified for reproduction. The cytogenetic screening program for young boars, carried out using continually refined diagnostic techniques, permits a precise and reliable karyotype assessment, identification of chromosomal abnormalities, and formulation of specific selection guidelines.

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Incidence, Reproductive Outcome, and Economic Impact of Reciprocal Translocations in the Domestic Pig

DNA ◽

10.3390/dna1020007 ◽

2021 ◽

Vol 1 (2) ◽

pp. 68-76

Author(s):

Nicole M. Lewis ◽

Claudia C. Rathje ◽

Carla Canedo-Ribeiro ◽

Lisa M. Bosman ◽

Lucas G. Kiazim ◽

...

Keyword(s):

Economic Impact ◽

De Novo ◽

Chromosomal Abnormalities ◽

In Situ Hybridisation ◽

Economic Losses ◽

Fluorescence In Situ Hybridisation ◽

Domestic Pig ◽

Reciprocal Translocations ◽

Cytogenetic Investigation

Pigs (Sus scrofa) have vast economic importance, with pork accounting for over 30% of the global meat consumption. Chromosomal abnormalities, and in particular reciprocal translocations (RTs), are an important cause of hypoprolificacy (litter size reduction) in pigs. However, these do not necessarily present with a recognizable phenotype and may cause significant economic losses for breeders when undetected. Here, we present a reappraisal of the incidence of RTs across several European pig herds, using contemporary methodology, as well as an analysis modelling the economic impact of these abnormalities. Molecular cytogenetic investigation was completed by karyotyping and/or multiprobe FISH (fluorescence in situ hybridisation) between 2016–2021, testing 2673 animals. We identified 19 types of chromosome abnormalities, the prevalence of these errors in the database was 9.1%, and the estimated incidence of de novo errors was 0.90%. Financial modelling across different scenarios revealed the potential economic impact of an undetected RT, ranging from £69,802 for an individual affected terminal boar in a commercial farm selling weaned pigs, to £51,215,378 for a genetics company with an undetected RT in a dam line boar used in a nucleus farm. Moreover, the added benefits of screening by FISH instead of karyotyping were estimated, providing a strong case for proactive screening by this approach.

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Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

Animals ◽

10.3390/ani11030904 ◽

2021 ◽

Vol 11 (3) ◽

pp. 904

Author(s):

Saif ur Rehman ◽

Faiz-ul Hassan ◽

Xier Luo ◽

Zhipeng Li ◽

Qingyou Liu

Keyword(s):

Selective Breeding ◽

Reference Genome ◽

De Novo ◽

Phenotypic Diversity ◽

Molecular Data ◽

Genomic Diversity ◽

Production Performance ◽

Phylogeographic Structure ◽

Economic Significance ◽

And Performance

The buffalo was domesticated around 3000–6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Nature Communications ◽

10.1038/s41467-020-20536-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zev N. Kronenberg ◽

Arang Rhie ◽

Sergey Koren ◽

Gregory T. Concepcion ◽

Paul Peluso ◽

...

Keyword(s):

Zebra Finch ◽

Cultured Cells ◽

De Novo ◽

Single Cells ◽

Variant Calling ◽

Chromatin Interaction ◽

Extended Haplotype ◽

Benchmark Datasets ◽

And Performance ◽

Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

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Assessment of a change of protocol of prenatal screening by inclusion of non-invasive prenatal diagnosis

Advances in Laboratory Medicine / Avances en Medicina de Laboratorio ◽

10.1515/almed-2020-0011 ◽

2020 ◽

Vol 1 (2) ◽

Author(s):

Rocío Cabra-Rodríguez ◽

Guadalupe Bueno Rodríguez ◽

Cristina Santos Rosa ◽

Miguel Ángel Castaño López ◽

Sonia Delgado Muñoz ◽

...

Keyword(s):

Prenatal Screening ◽

Chromosomal Abnormalities ◽

Screening Program ◽

High Sensitivity ◽

Maternal Blood ◽

Screening Tests ◽

Loss To Follow Up ◽

Non Invasive ◽

Second Trimester Screening ◽

Trimester Screening

AbstractObjectivesNon-invasive prenatal screening (NIPS) is a test for the detection of major fetal chromosomal abnormalities in maternal blood during pregnancy. The purpose of this study was to assess the performance of NIPS implemented within the framework of the Screening Program for Congenital Abnormalities of the Andalusian Health System.MethodsA retrospective observational study was undertaken to determine the number of NIPS tests performed since its introduction. The number of invasive diagnostic tests done after the implementation of NIPS in the patients included in the program between March 2016 and August 2017 was also quantified.ResultsA total of 6,258 combined first- and second trimester screening tests were performed, covering 95% of the population. In total, 250 subjects were identified as high risk, of whom 200 underwent NIPS after loss to follow-up. NIPS showed a sensitivity of 100% (95% CI: 76.84–100%) and a specificity of 99.46% (95% CI: 97.04–99.99%).ConclusionsThis test has proven to have a very high sensitivity and specificity. The results obtained demonstrate that the incorporation of NIPS in clinical practice minimizes the rate of miscarriages and reduces the frequency of invasive procedures by 70%.

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De novo adult acute myeloid leukemia with two new mutations in juxtatransmembrane domain of the FLT3 gene: a case report

Journal of Medical Case Reports ◽

10.1186/s13256-020-02587-3 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Ismael F. Alarbeed ◽

Abdulsamad Wafa ◽

Faten Moassass ◽

Bassel Al-Halabi ◽

Walid Al-Achkar ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

De Novo ◽

Chromosomal Abnormalities ◽

Molecular Genetic ◽

Type A ◽

Chemotherapeutic Treatment ◽

Acute Myeloid ◽

New Mutations

Abstract Background Approximately 30% of adult acute myeloid leukemia (AML) acquire within fms-like tyrosine kinase 3 gene (FLT3) internal tandem duplications (FLT3/ITDs) in their juxtamembrane domain (JMD). FLT3/ITDs range in size from three to hundreds of nucleotides, and confer an adverse prognosis. Studies on a possible relationship between of FLT3/ITDs length and clinical outcomes in those AML patients were inconclusive, yet. Case presentation Here we report a 54-year-old Arab male diagnosed with AML who had two FLT3-ITD mutations in addition to NPM1 mutation. Cytogenetic approaches (banding cytogenetics) and fluorescence in situ hybridization (FISH) using specific probes to detect translocations t(8;21), t(15;17), t(16;16), t(12;21), and deletion del(13q)) were applied to exclude chromosomal abnormalities. Molecular genetic approaches (polymerase chain reaction (PCR) and the Sanger sequencing) identified a yet unreported combination of two new mutations in FLT3-ITDs. The first mutation induced a frameshift in JMD, and the second led to a homozygous substitution of c.1836T>A (p.F612L) also in JMD. Additionally a NPM1 type A mutation was detected. The first chemotherapeutic treatment was successful, but 1 month after the initial diagnosis, the patient experienced a relapse and unfortunately died. Conclusions To the best of our knowledge, a combination of two FLT3-ITD mutations in JMD together with an NPM1 type A mutation were not previously reported in adult AML. Further studies are necessary to prove or rule out whether the size of these FLT3-ITDs mutations and potential other double mutations in FLT3-ITD are correlated with the observed adverse outcome.

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Cerebral arteriopathy in ACTA2 mutations: a spectrum of disease highlighted by a case of variable penetrance in two siblings

Journal of Neurosurgery Pediatrics ◽

10.3171/2020.8.peds20391 ◽

2021 ◽

pp. 1-6

Author(s):

Christine Tschoe ◽

Teddy E. Kim ◽

Kyle M. Fargen ◽

Stacey Q. Wolfe

Keyword(s):

Moyamoya Disease ◽

De Novo ◽

Early Recognition ◽

Smooth Muscle Actin ◽

Amino Acid Replacement ◽

Single Mutation ◽

Cerebral Arteriopathy ◽

And Performance ◽

Actin Protein ◽

Revascularization Procedures

Until recently, cerebral arteriopathy due to heterozygous mutations of the ACTA2 gene was considered a variant of moyamoya disease. However, radiographic analysis of patients with these mutations reveals a distinctive angiographic appearance from that seen in moyamoya disease. Several heterozygous missense ACTA2 mutations have been implicated in the development of this distinct cerebrovascular entity; however, the penetrance and systemic manifestations of these mutations vary based on the location of the amino acid replacement within the α–smooth muscle actin protein. The severity of the phenotype may also differ among patients within a single mutation type. There is limited literature on the safety and efficacy of revascularization procedures for ACTA2 arteriopathy, which have been limited to those patients with known Arg179His mutations. The authors provide a review of the breadth of mutations within the ACTA2 literature and report a case of two siblings with de novo ACTA2 Arg258Cys mutations with differing clinical courses, highlighting the utility of indirect revascularization with 8-year follow-up data. This case highlights the importance of early recognition of the angiographic appearance of ACTA2 cerebral arteriopathy and performance of genetic testing, as the location of the mutation impacts clinical presentation and outcomes.

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Chromosomal abnormalities in recurrent miscarriages by conventional karyotyping analysis

Revista Brasileira de Saúde Materno Infantil ◽

10.1590/1806-93042018000200002 ◽

2018 ◽

Vol 18 (2) ◽

pp. 265-276 ◽

Cited By ~ 1

Author(s):

Alessandra Bernadete Trovó de Marqui

Keyword(s):

Genetic Counseling ◽

Chromosomal Abnormality ◽

Pregnancy Loss ◽

Chromosomal Abnormalities ◽

Recurrent Miscarriage ◽

Virtual Library ◽

Reciprocal Translocations ◽

Recurrent Miscarriages ◽

Monosomy X ◽

Products Of Conception

Abstract Objectives: to describe the prevalence and types of chromosomal abnormalities in couples with recurrent miscarriage and products of conception. Methods: electronic searches were performed in the PubMed/Medline database and in the Portal Regional da Biblioteca Virtual em Saúde/BVS (Regional Website of the Virtual Library in Health/BVS) using the descriptors “chromosomal abnormalities and abortions and prevalence”. After applying the inclusion and exclusion criterias, 17 studies were selected. Results: 11 studies were conducted in couples with recurrent miscarriage and six in products of conception. The main results of the couples with recurrent miscarriage were: the frequency of chromosomal abnormalities which varied from 1.23% to 12% and there was a predominance alteration of the chromosomal structures (reciprocal translocations, followed by Robertsonian). In products of conception, the results observed were: the frequency of chromosomal abnormality was above 50% in approximately 70% of the studies; there was a predominance alteration of the numerical chromosomal (trisomy - chromosomes 16, 18, 21 and 22, followed by polyploidy and monosomy X). Conclusions: in summary, cytogenetic alterations represent an importante cause of pregnancy loss and its detection can help couples with genetic counseling. Therefore, the value of knowledge on the prevalence of cytogenetic abnormalities in miscarriage samples is unquestionable, once it is permitted a proper genetic counseling for the couple.

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Breast Cancer Screening Program in Morocco: Status of implementation, organization and performance

International Journal of Cancer ◽

10.1002/ijc.31749 ◽

2018 ◽

Vol 143 (12) ◽

pp. 3273-3280 ◽

Cited By ~ 7

Author(s):

Partha Basu ◽

Farida Selmouni ◽

Latifa Belakhel ◽

Catherine Sauvaget ◽

Loubna Abousselham ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Screening ◽

Breast Cancer Screening ◽

Screening Program ◽

Breast Cancer Screening Program ◽

Cancer Screening Program ◽

And Performance

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Clinical, morphologic, and cytogenetic characteristics of 26 patients with acute erythroblastic leukemia

Blood ◽

10.1182/blood.v80.11.2873.2873 ◽

1992 ◽

Vol 80 (11) ◽

pp. 2873-2882 ◽

Cited By ~ 75

Author(s):

OI Olopade ◽

M Thangavelu ◽

RA Larson ◽

R Mick ◽

A Kowal-Vern ◽

...

Keyword(s):

Myeloid Leukemia ◽

De Novo ◽

Chromosomal Abnormalities ◽

Normal Karyotype ◽

Intensive Chemotherapy ◽

Trisomy 8 ◽

Cytogenetic Abnormalities ◽

Favorable Prognosis ◽

Multiple Abnormalities ◽

French American British

Abstract We have performed a retrospective analysis of the clinical, morphologic, and cytogenetic findings in 26 patients diagnosed between January 1969 and September 1991 with acute erythroblastic leukemia de novo (EL or AML-M6). Clonal chromosomal abnormalities were found in 20 (77%) patients (95% confidence interval [CI], 61% to 93%). Loss of all or part of the long arm (q) of chromosomes 5 and/or 7 was observed in 17 (65%) patients (95% CI, 47% to 83%). In addition, the karyotypes were often complex, with multiple abnormalities and subclones. Among the remaining nine patients, six had a normal karyotype and one each had trisomy 8, t(3;3), or t(3;5). The overall frequency of abnormalities of chromosomes 5 and/or 7 observed in our M6 patients is similar to that observed in our patients with therapy-related acute myeloid leukemia (t-AML; 99 of 129 patients, 77%), but substantially higher than that noted in our other patients with AML de novo (French- American-British [FAB] subtypes M1-M5: 52 of 334 patients, 16%). Our M6 patients with abnormalities of chromosomes 5 and/or 7 were older and had a shorter median survival (16 v 77 weeks [P = .005]) than did the M6 patients without these abnormalities. We found no correlation between morphologic features and either cytogenetic abnormalities or clinical outcome. Of note was the finding that the percentage of myeloblasts, which may account for only a small fraction of the total marrow elements when the revised FAB criteria are applied, had no bearing on prognosis. We conclude that acute erythroblastic leukemia, when defined by morphologic criteria, consists of two distinctive subgroups: one group tends to be older, has complex cytogenetic abnormalities, especially of chromosomes 5 and/or 7, and shares biologic and clinical features with t-AML; the other group, with simple or no detectable cytogenetic abnormalities, has a more favorable prognosis when treated with intensive chemotherapy.

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Reproductive strategies and chromosomal aberrations affect survival in the Rivuliid fish Hypsolebias sertanejo

Zygote ◽

10.1017/s0967199420000362 ◽

2020 ◽

pp. 1-7

Author(s):

Mariana Machado Evangelista ◽

Elizabeth Romagosa ◽

Diógenes Henrique Siqueira-Silva ◽

George Shigueki Yasui ◽

Takafumi Fujimoto ◽

...

Keyword(s):

Flow Cytometry ◽

Reproductive Success ◽

Reproductive Strategies ◽

Chromosomal Abnormalities ◽

Reproductive Behaviour ◽

Conservation Strategies ◽

Hatching Rate ◽

Natural Conditions ◽

And Performance ◽

Ploidy Status

Summary Rivulidae comprises a family of fish largely distributed in Brazil that includes 201 species, of which 125 are considered endangered. This fact emphasizes the need for development of conservation strategies including studies on genetics and reproduction. In this paper, we describe aspects of biology and reproduction of the rivuliid species Hypsolebias sertanejo. We outline the reproductive behaviour of this species under laboratory conditions, analyze ploidy status by flow cytometry, describe reproductive behaviour and performance and test dry and wet incubation of eggs. Although H. sertanejo showed well known patterns of reproductive behaviour, we verified many peculiarities inherent to its reproductive biology. As expected, most individuals were diploid (87.71%), however 14.29% were considered mosaics. Although no sterility was observed within mosaics, infertility of these fish was not fully evaluated. Hatching rate of the eggs collected was very low following both dry and wet incubation (5.04 and 3.79%, respectively). These results provide interesting information regarding the reproductive success of this species, and suggest that chromosomal abnormalities described may reduce the survival of H. sertanejo under natural conditions, limiting the perpetuation of this species, and emphasizing the need for more preservation efforts, including artificial propagation and gene banking.

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