PGT-M for spinocerebellar ataxia type 1: development of a STR panel and a report of two clinical cases

PURPOSE

To present the developed preimplantation genetic testing (PGT) for spinocerebellar ataxia type 1 (SCA1) and the outcomes of IVF with PGT.

METHODS

PGT was performed for two unrelated couples from the Republic of Sakha (Yakutia) with the risk of SCA1 in one spouse. We have developed a system for PGT of a monogenic disease (PGT-M) for SCA1, which includes the analysis of a panel of 11 polymorphic STR markers linked to the ATXN1 gene and a pathogenic variant of the ATXN1 gene using nested PCR and fragment analysis. IVF/ICSI programs were performed according to standard protocols. Multiple displacement amplification (MDA) was used for whole genome amplification (WGA) and array comparative genomic hybridization (aCGH) for aneuploidy testing (PGT-A).

RESULTS

Eight STRs were informative for the first couple and ten for the second. Similarity of the haplotypes carrying pathogenic variants of the ATXN1 gene was noted. In the first case, during IVF/ICSI-PGT, three embryos reached the blastocyst stage and were biopsied. One embryo was diagnosed as normal by maternal STR haplotype and the ATXN1 allele. PGT-A revealed euploidy. The embryo transfer resulted in a singleton pregnancy, and a healthy boy was born. Postnatal diagnosis confirmed normal ATXN1. In the second case, two blastocysts were biopsied. Both were diagnosed as normal by PGT-M, but PGT-A revealed aneuploidy.

CONCLUSION

Birth of a healthy child after PGT for SCA1 was the first case of successful preimplantation prevention of SCA1 for the Yakut couple and the first case of successful PGT for SCA1 in Russia.

The last flight of F/O Tadeusz Stabrowski. Identification of the polish pilot

The paper presents the process of identifying an unnamed soldier of the Polish armed forces in the west, whose remains were found in a nameless grave at the municipal cemetery in Le Crotoy in France. The Polish Genetic Database of Victims of Totalitarianism team carried out the research in cooperation with the Ministry of Culture and National Heritage. A comprehensive analysis of autosomal and Y-STR markers was performed. Historical, anthropological, and forensic examinations of the remains were also carried out. The items found with the remains were also examined. Identification based on DNA analysis made it possible to restore the identity of the Polish pilot who died on 11 March 1943 near the French coast, F/O Tadeusz Stabrowski. The airman regained his name in 2018, he was about 26 years old at the time of his death and left behind a grieving wife and son in the United Kingdom. The success of identifying the NN remains was guaranteed by the appointment of an interdisciplinary team consisting of specialists in archaeology, anthropology, history, forensic medicine and forensic genetics. The analysis of historical sources allowed to determine 4 missing airmen whose remains could have been buried in the cemetery in Le Crotoy. An interesting aspect of the research was the cooperation with history enthusiasts and fans of Polish aviation, thanks to which it was finally possible to narrow down the group of pilots sought and reach the family of Tadeusz Stabrowski, who submitted comparative material for research. This is the first case of establishing the identity of a Polish pilot killed in France. Many institutions have been involved in the project, including Polish Ministry of Culture and National Heritage (MDiKN), which partially funded the research.

A genogeographic study of the Kyrgyz mountain merino via microsatellite markers

The aim was to ascertain the genetic and geographical structure of the Kyrgyz mountain merino (KMM). We analyzed DNA samples of 109 Kyrgyz mountain merino specimens, bred in three state breeding factories (STB), including "Orgochor" in the Issykul Province, "Katta-Taldyk" in the Osh Province and STb named after Luschikhin in the Talas Province. We identified 126 alleles in 12 microsatellite markers (McM042, INRA006, McM527, ETH152, CSRD247, OarFCB20, INRA172, INRA063, MAF065, MAF214, INRA005, INRA023). There were 6 to 16 alleles in each locus (mean 10.500 ± 0.957 alleles per locus). We identified 67 rare alleles (prevalence less than 5.0 %), which made up 53.2 % of all alleles found. The greatest number of rare alleles was found in STR-markers of CSRD247, INRA023, INRA005, INRA006, MAF214 and OarFCB20. For each group, there were individual differences in the distribution of allele frequencies across all the STR loci studied. The most significant of them were as follows: with regard to the McM042 locus, allele 87 was major in the TALAS and OSH groups (35.6 and 45.7 %, respectively), whereas allele 95 was major in the ISSYK- KUL group (36.2 %); allele 154 was major in all groups with regard to the INRA172 locus, but it was 1.25 times less prevalent in the ISSYK-KUL and 1.66 times less prevalent in the OSH groups compared to TALAS (55.2 and 41.4 %, respectively), whereas alleles 156 and 158 were found only in the ISSYK-KUL group. Considering the ETH152 locus, 186 allele prevalence in the TALAS group was 51.1 %, but allele 190 was also markedly prevalent in the ISSYK-KUL and OSH groups, 34.5 and 34.3 %, respectively. The genetic division of the studied groups of KMM (with K from 3 to 10) was homogeneous - the contribution of each subcluster was equivalent. The AMOVA analysis revealed that the groups are located equidistantly. To conclude, the genetic diversity of the Kyrgyz mountain merino in three state breeding factories of the Kyrgyz Republic was high and comparable with each other.

Kinship analysis of skeletal remains from the Middle Ages

Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.

Genetic Heterogeneity of X-Linked Ichthyosis in the Republic of North Ossetia-Alania, Case Series Report

North Caucasus has always been a residence of a lot of different authentic ethnic groups speaking different languages and still living their traditional lifestyle. The diversity appeared to be reflected in the accumulation of different mutations causing common inherited disorders. X-linked ichthyosis represents the second most common form of genodermatoses after ichthyosis vulgaris. Eight patients from three unrelated families of different ethnic origin, Kumyk, Turkish Meskhetians, and Ossetian, with X-linked ichthyosis from the North Caucasian Republic of North Ossetia-Alania were examined. NGS technology was implied for searching for disease-causing variants in one of the index patients. Known pathogenic hemizygous deletion in the short arm of chromosome X encompassing the STS gene was defined in the Kumyk family. A further analysis allowed us to establish that likely the same deletion was a cause of ichthyosis in a family belonging to the Turkish Meskhetians ethnic group. In the Ossetian family, a likely pathogenic nucleotide substitution in the STS gene was defined; it segregated with the disease in the family. We molecularly confirmed XLI in eight patients from three examined families. Though in two families, Kumyk and Turkish Meskhetian, we revealed similar hemizygous deletions in the short arm of chromosome X, but their common origin was not likely. Forensic STR markers of the alleles carrying the deletion were defined to be different. However, here, common alleles haplotype is hard to track for a high local recombination rate. We supposed the deletion could arise as a de novo event in a recombination hot spot in the described and in other populations with a recurrent character. Defined here are the different molecular genetic causes of X-linked ichthyosis in families of different ethnic origins sharing the same residence place in the Republic of North Ossetia-Alania which could point to the existing reproductive barriers even inside close neighborhoods.

Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

Cell-based non-invasive prenatal testing for monogenic disorders: confirmation of unaffected fetuses following preimplantation genetic testing

PURPOSE

Proof of concept of the use of cell-based non-invasive prenatal testing (cbNIPT) as an alternative to chorionic villus sampling (CVS) following preimplantation genetic testing for monogenic disorders (PGT-M).

METHOD

PGT-M was performed by combined testing of short tandem repeat (STR) markers and direct mutation detection, followed by transfer of an unaffected embryo. Patients who opted for follow-up of PGT-M by CVS had blood sampled, from which potential fetal extravillous throphoblast cells were isolated. The cell origin and mutational status were determined by combined testing of STR markers and direct mutation detection using the same setup as during PGT. The cbNIPT results with respect to the mutational status were compared to those of genetic testing of the CVS.

RESULTS

Eight patients had blood collected between gestational weeks 10 and 13, from which 33 potential fetal cell samples were isolated. Twenty-seven out of 33 isolated cell samples were successfully tested (82%), of which 24 were of fetal origin (89%). This corresponds to a median of 2.5 successfully tested fetal cell samples per case (range 1-6). All fetal cell samples had a genetic profile identical to that of the transferred embryo confirming a pregnancy with an unaffected fetus, in accordance with the CVS results.

CONCLUSION

These findings show that although measures are needed to enhance the test success rate and the number of cells identified, cbNIPT is a promising alternative to CVS.

TRIAL REGISTRATION NUMBER

N-20180001.

Characterization of a new human astrocytoma cell line SHG140: cell proliferation, cell phenotype, karyotype, STR markers and tumorigenicity analysis

Background: Primary tumor Cell was an important tool for tumor research. Here, a new astrocytoma cell line SHG-140 was established and its proliferation, phenotype, karyotype, STR authentication, pathological characteristics, and characteristics of the cells' intrancranial xenografts of nude mice were studied.

Methods: Primary SHG-140 culture was performed in DMEM/F12 medium with 10% FBS. Cell proliferation, karyotype analysis, cell immunofluorescence and STR authentication of SHG140 cells were performed. HE staining and immunohistochemistry, Whole oncogene high flux sequencing of the patient sample were carried out. SHG140 cells were injected into the brain of nude mice, HE staining and immunohistochemistry of intracranial xenograft tumor were detected.

Results: Cell immunofluorescence demonstrated that SHG140 cells were positive for A2B5 (Glial precursors ganglioside), GFAP (Glial fibrillary acidic protein), Nestin, S-100 (Acid calcium bingding protein), Olig2 (Oligodendrocyte transcription factor 2) and Ki67 (Nuclear-associated antigen), cells negatively stained for Vimentin. Cell proliferation curve revealed that SHG140 proliferated slightly within 48 h, which then significantly proliferated to the fourth day. Karyotype analysis demonstrated its total number of chromosomes was 55, having trisomy of chromosome 6, 7, 8, 9 and X, and tetrad of chromosome 1 and 21, chromosomal deletion and rearrangement were observed. STR markers analysis showed the cells were derived from human male. SHG140 cells had tumorigenic properties - the intracranial injection of these cells into nude mice gave rise to growing tumors. We found that the glioma tissue was diffusively positive for GFAP, Nestin, slightly positive for Olig2, S-100; the positive rate of Ki-67 was 65% and negative for Vimentin. SHG140 cells were tumorigenic, GFAP, Nestin, S-100 Olig-2, the proliferation marker Ki-67 were expressed in its intracranial xenograft, Vimentin was negative expressed. Whole oncogene high flux sequencing of the patient tissue showed TP53, PTEN, IDH1 and PTCH1 mutation were existed.

Conclusions: Our study showed that SHG140 was an astrocytoma glioma continuous cell line derived from a human adult male, having a strong tumorigenicity in nude mice, which made it wound be a useful model for the study of human glioblastoma multiforme.

Allelic frequencies with 23 autosomic STRS in the Aymara population of Peru

Population data of the Aymara in the province of Puno were established for 23 autosomal STR markers. DNA was obtained from unrelated individuals (n = 190) who reside in three areas of the Floating Islands of Lake Titicaca, residents on the border with Bolivia and residents who are not from the border with Bolivia. The PENTA E marker presented the highest PD (0.9738), PIC (0.8793), and PM (0.7847) values. The combined PD was greater than 0.99999999 and the combined PE was 0.99999994. The largest distance, based on Fst values, was between the Aymara population and the Ashaninca population (0.04022), and the smallest distance was with the populations of Bolivia (0.00136) and Peru (0.00525).

Population genetic study of a Peruvian population using human identification STRs

In this study, allele frequencies were determined in a Peruvian population for application to human identification. A population of 601 unrelated individuals was analyzed (400 individuals with the GlobalFiler Express kit and 201 individuals with the VeriFiler Express kit). The locus with the highest power of discrimination (PD) was SE33 (0.9851, 31 alleles), while the least polymorphic locus was D22S1045 (0.75810, 11 alleles). The PE in a similar fashion ranged from 0.2421 (D22S1045) to 0.7818 (SE33). Under the assumption of independence, the combined PD was > 0.9999999999 while the combined PE = 0.9999999933. When comparing the population studied with different populations of Latin America, the greatest Fst genetic distance was obtained with a Venezuelan population (0.052), and the shortest distance was with a Bolivian and Peruvian population (0.004).

Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers

The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents' genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population's genetic diversity and structure should be monitored regularly.

Putative founder effect in the Polish, Iranian and United States populations for the L144S SOD1 mutation associated with slowly uniform phenotype of amyotrophic lateral sclerosis

Mutations in SOD1 cause approximately 12-25% of familial ALS and ≈2% of apparently sporadic ALS cases. Clinical phenotypes linked to SOD1 mutations are heterogeneous and intra-familial variability of the clinical phenotype is frequently observed. SOD1 L144S mutation, identified also in Brazil, Iran and United States, is the second most frequent mutation among ALS patients in Poland. So far, 10 FALS pedigrees with SOD1 L144S mutation have been reported worldwide. The aim of the study was to establish the origin of SOD1 L144S mutation in geographically distinct populations. The clinical presentation of the Polish patients was compared with those from the previously reported populations (26 ever-reported patients). Clinically, L144S mutation is associated with both sporadic and familial ALS of relatively slow uniform course, a prevalent onset in the lower limbs, either classic or PMA presentation and a long survival time. Like in the case of other previously described SOD1 mutations, there was an intra-familial heterogeneity and reduced penetrance for ALS was observed. We propose that the L144S SOD1 mutation in the three studied populations has a common founder most likely of Polish origin.

German population data for 18 X-STRs: a hexaplex PCR adding two clusters of X-STRs to the Argus X-12 set and expanding the German haplotype databases

In kinship analysis, large data sets with estimated haplotype frequencies for marker clusters are very important for the likelihood calculation. Practical use of the X-STRs demonstrated that in some complex kinship cases, the marker set of the Investigator Argus X-12 kit can be insufficient. This study aimed to extend the German data base of the Argus X-12 kit (1037 haplotypes) and for a cluster in Xq21 (806 haplotypes) with additional 700 male haplotypes and to include a further cluster in Xp22.3 to complete the X-STR marker set for complex kinship cases.

Evaluation of loss of heterozygosity of chromosome 22q11.21 region in patients with congenital heart diseases

The 22q11.21 region is prone to low-copy repeats events that lead to congenital anomaly disorders. We tested genomic DNA of 20 families with non-syndromic CHD patients using a set of three known consecutive high polymorphic short tandem repeat (STR) markers along the 22q11.21 region; D22S941, D22S944 and D22S264 loci. We found loss of heterozygosity (LOH) in D22S941 locus in 2 out of 20 families (10%) with 2 offspring affected by ASD combined with PS and TOF respectively. No LOH found in D22S944 and D22S264 loci either in affected cases or control group and no LOH found in D22S941 in the control group. Also we observed that D22S944 locus prone to be less allele diversity than D22S941 and D22S264 loci.

Molecular genetic study of Calpainopathy in Iran

INTRODUCTION

Calpainopathy is an autosomal recessive form of limb girdle muscular dystrophies (LGMDs) caused by mutations in the CAPN3 gene. CAPN3 is a Ca²⁺-dependent cystein protease consisting of 821 amino acids. LGMD is a highly heterogeneous disorder and mutation identification of this disease by Sanger sequencing of all genes is expensive and time consuming. Using autozygosity mapping is an effective approach to address this issue.

METHODS

We used two sets of multiplex STR (Short tandem repeat) markers linked to CAPN3, DYSF, SGCA, SGCB, SGCG, SGCD genes following sequencing of the CAPN3 gene. In silico analysis and mutation detection in one hundred ethnically matched healthy individuals were carried out to determine the pathogenicity of novel mutations. Sequence variant interpretation was performed using the American College of Medical Genetics and Genomics (ACMG) guideline.

RESULTS

Sixteen out of 50 families linked to the CAPN3 gene. In this study, mutations were found in 14 out of 16 families including 4 novel (c.1894A > T, c.567delG, c.2254-2256delAAC, and c.2373C > T) and 9 previously reported mutations consisting of 5 missense (c.2105C > T, c.2243G > A, c.1714C > T, c.291C > A, c.956C > T), 3 splice site (c.2380 + 2 T > G, c.946-2A > G, c.380G > A), and one indel (c.2257delinsAA) mutations.

DISCUSSION

The c.2105C > T was found to be the most frequent mutation in this study. The results of this study revealed that most cases with splicing, frame shift and nonsense mutations experienced more severe clinical manifestations. Nonetheless, this should be confirmed by further studies on larger sample size.

Novel Multiplex Fluorescent PCR-Based Method for HLA Typing and Preimplantational Genetic Diagnosis of β-Thalassemia

BACKGROUND AND AIMS

Thalassemia is curable by bone marrow transplantation; however, finding suitable donors with defined HLA combination remains a major challenge. Cord blood stem cells with preselected HLA system through preimplantation genetic diagnosis (PGD) proved very useful for resolving scarce HLA-matched bone marrow donors.

METHODS

A thalassemia trait couple with an affected child was included in this study. We used informative STR markers at the HLA and beta globin loci to develop a single cell multiplex fluorescent PCR protocol. The protocol was extensively optimized on single lymphocytes isolated from the couple's peripheral blood. The optimized protocol was applied on single blastomeres biopsied from day 3 cleavage stage IVF embryos of the couple.

RESULTS

Four IVF embryos biopsied on day 3 and a single blastomere of each were provided for genetic diagnosis of combined β-thalassemia mutations and HLA typing. Of these, one embryo was diagnosed as homozygous normal for the thalassemia mutation and HLA matched with the existing affected sibling.

CONCLUSION

The optimized protocol worked well in PGD clinical cycle for selection of thalassemia-unaffected embryos with the desired HLA system.

Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

Frequency of Y Chromosome Microdeletions Among Iranian Infertile Men with Azoospermia and Severe Oligozoospermia: A Meta-analysis

BACKGROUND

While multiple factors can contribute to male infertility, genetic factors, such as chromosomal disorders or Y-chromosome microdeletion, are responsible for about 10% of male infertility. Considering the role of Y-chromosome micro-deletions in men with oligozoospermia who volunteer for in vitro fertilization (IVF), the prevalence of such microdeletions in each particular community needs to be exactly determined. Hence, the present study attempted to analyze the available literature on the frequency of chromosome microdeletion among Iranian infertile men.

METHODS

In the first stage, a systematic search was performed on international and Iranian databases including PubMed, Scopus, Web of Science, IranMedex, MEDLIB, and Scientific Information Database in order to extract all relevant studies published until December 1, 2014.

RESULTS

According to the literature review and meta-analysis process, Y chromosome microdeletions were present in about 12.1% (95% CI, 6.5-21.5) of Iranian infertile men with azoospermia and severe oligozoospermia.

CONCLUSION

Because of the presence of Y-chromosome microdeletion in at least 12% of Iranian infertile men, it is necessary all the IVF centers, implement this Y-chromosome microdeletion screening tests in the work-up of male infertility.