Lineage marker as a key player in complex forensic cases from the perspective of Y chromosome

Kako se Y hromozom kroz generacije ne menja rekombinacijama, prenosi se uglavnom nepromenjen sa oca na sina. Haplotipovi dobijeni kombinovanom analizom kratkih tandemskih ponovaka na Y hromozomu imaju široku primenu u forenzičkim analizama za definisanje paternalne linije muškog donora biološkog traga, posebno u slučajevima gde standardna analiza autozomnih markera nije dovoljno informativna. Y vezani haplotipovi se koriste i u evolucionim i genealoškim studijama, ali se za rekonstrukciju filogenije Y hromozoma koristi analiza polimorfizama pojedinačnih nukleotida. Promene na Y hromozomu se ipak dešavaju usled mutacija što može da dovede do diferencijacije Y vezanih haplotipova između oca i sinova. Tako mutacije u lokusima sa kratkim tandemskim ponovcima mogu da omoguće identifikaciju muškarca u okviru jedne paternalne linije, ali mogu i da dovedu do progrešnog isključenja biološkog srodstva. Usled toga je za tačnu interpretaciju genetičkih profila neophodna precizna procena stope mutacije pojedinačnih lokusa, za šta se koriste studije parova otac-sin ili velikih porodični stabala.Y chromosome is transmitted mostly unchanged from father to son due to the absence of recombination events. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms are widely used to define paternal line of unknown male perpetrator in forensic analysis, especially when standard analysis of autosomal markers is not informative enough. Y-chromosomal haplotypes are also used in evolutionary and genealogical studies, but single nucleotide polymorphisms are more suitable for the reconstruction of the Y chromosome phylogeny. However, Y chromosome changes due to mutations, which could lead to differentiation of Y haplotypes between father and sons. Thus, mutations in short tandem repeats loci can enable the identification of a man within a single paternal line, but they could also lead to an erroneous exclusion of biological paternity. Reliable mutation rates, for the proper use and accurate interpretation of genetic profiles, could be estimated from multi-generation pedigrees or father-son pairs

Genetics of inherited peripheral neuropathies: renewed data

Nasledne periferne neuropatije čini klinički i genetički heterogena grupa bolesti uzrokovanih aksonalnom degeneracijom motornih i senzornih neurona perifernog nervnog sistema. Odlikuju se izrazitom alelskom i lokusnom heterogenošću, a do danas je sa ovom grupom bolesti asocirano više od 1000 mutacija u preko 100 gena. Korišćenjem klasičnih metoda genetičke dijagnostike najveći broj uzročnih mutacija identifikovan je u 4 gena: PMP22, GJB1, MFN2 i MPZ. Najučestaliji tip, CMT1A, uzrokovan je duplikacijom 1,5 Mb u regionu hromozoma 17p11.2 i čini oko 50% svih naslednih perifernih neuropatija. Ovom duplikacijom obuhvaćen je gen PMP22 koji kodira protein mijelinskog omotača. Recipročna delecija ovog regiona asocirana je sa blagom naslednom neuropatijom. Geni GJB1, MFN2 i MPZ se karakterišu širokim spektrom mutacija, a populacione specifičnosti u vidu značajnih odstupanja u zastupljenosti pojedinih mutacija se mogu objasniti efektom osnivača. Upotrebom masivnog paralelnog sekvenciranja omogućen je napredak u genetičkoj dijagnostici ovih bolesti koji se pre svega ogleda u otkriću novih gena, kao i u otkriću novih mutacija u genima odranije asociranim sa ovim, ali i sa drugim neurološkim i mišićnim bolestima. Pri tome, verovatnoća za otkrivanje uzročne mutacije koreliše sa pozitivnom porodičnom anamnezom, prisustvom endogamije, ranim početkom i demijelinirajućim oblikom bolesti. Takođe, kod nekih bolesnika je identifikovano i prisustvo strukturnih varijacija koje ne obuhvataju do sada poznate uzroke naslednih perifernih neuropatija, kod kojih je patomehanizam nastanka bolesti i dalje nepoznat.Inherited peripheral neuropathies (IPN) comprise a clinicaly and geneticaly heterogenous group of disorders caused by axonal degeneration of motor and sensory nerves of peripheral nervous system. So far, more than 1000 mutations in more then 100 genes has been found to be associated with IPN. Using standard molecular-genetic diagnostics, vast number of mutations was identified in following genes: PMP22, GJB1, MFN2 and MPZ. The most frequent, CMT1A, is caused by 1,5 Mbp duplication of 17p11.2 and represents aproximatelly 50% of all IPN. The duplication includes myelin sheet protein gene PMP22, whereas reciprocal deletion is associated with a mild hereditary neuropathy termed HNPP. GJB1, MFN2 and MPZ genes harbour various mutations, whose frequencies vary between populations. Significant differences of individual mutation frequencies could be mostly explained by founder effect. Massive parallel sequencing methodologies (MPS) brought new discoveries. First of all, new genes were found to be associated with IPN. Then, new mutations in well-known genes previously associated with IPN, but also with other neurological and muscular disorders, were found to be disease-causing. Also, some patients were found to carry structural variants involving regions not previously associated with IPN, with pathomechanism of the disease yet to be resolved. Generally, a positive genetic diagnosis was more likely to be reached in cases with positive history of neuropathy and consanguinity, early onset and/or demyelinating neuropathy

Diagnostics of rare diseases new paradigm

Po definiciji, retke bolesti obuhvataju oboljenja čija je učestalost manja od 1 u 2000 u Evropi. Do sada je identifikovano skoro 7000 retkih bolesti uzrokovanih mutacijama u preko 4000 gena, a na svakih 50 osoba u Evropi jedna ima retku bolest za koju je pokazano ili se smatra da je genetički uzrokovana. Objavljivanje preliminarne sekvence humanog genoma 2001. godine, kao i automatizacija reakcija PCR-a i sekvenciranja, omogućilo je otkrivanje velikog broja gena uzročnika retkih bolesti, kao i uspostavljanje i široku primenu molekularno - genetičke dijagnostike. Na ovaj način je omogućena dijagnostika bolesti koje su se odlikovale relativno čestim pojavljivanjem, a koje nisu imale posebno izraženu alelsku ili lokusnu heterogenost. Razvoj metoda masivnog paralelnog sekvenciranja omogućio je širu dijagnostiku poznatih bolesti, ali se otvorila i mogućnost da se potraži uzrok za svaku retku bolest, međutim, nakon više od 10 godina masovne primene, preko 70% bolesti verovatno uzrokovanih naslednim faktorima i dalje ima nepoznatu etiologiju.Rare diseases comprise diseases with a frequency less than 1 in 2000 in Europe. So far, almost 7,000 rare diseases caused by mutations in over 4,000 genes have been identified, and for every 50 people in Europe, one has a probably genetically caused rare disease. The draft sequence of the human genome published in year 2001, as well as the automation of PCR and sequencing techniques enabled the identification of a large number of genes that cause rare diseases, as well as the establishment and wide application of molecular-genetic diagnostics. Thus, it was possible to establish the genetic background of relatively frequent and diseases without significant allelic or locus heterogeneity. The development of massive parallel sequencing methods has enabled a broader diagnosis of known diseases, but also enabled scientific community to look for the cause of each rare disease. However, after more than 10 years, over 70% of probably genetically caused diseases still have an unknown etiology

Schizophrenia and Apolipoprotein E Gene Polymorphism in Serbian Population

Apolipoprotein E (APOE) gene variants are associated with alterations in brain function and increased risk of Alzheimer's disease (AD) and conflicting results have been reported in schizophrenia. Our results showed no significant differences in APOE allele or genotype frequencies between the Serbian schizophrenic patients and control individuals. However, we observed a possible association between particular subtypes of schizophrenia and APOE epsilon 3/epsilon 3 genotype (p = .01221) and epsilon 4 allele showed a tendency toward positive association with responding to typical neuroleptics. APOE genotypes have no major influence on risk of schizophrenia, treatment and response to conventional antipsychotics, and age of onset in schizophrenia

Polymorphisms of the Prion Protein Gene (PRNP) in a Serbian Population

Prion diseases are a group of etiologically heterogenous neurodegenerative disorders. We have analyzed the coding region of PRNP gene in 121 healthy citizens of Serbia to determine whether the frequencies of M129V, E219K, and octapeptide repeat number polymorphism. For Serbian population, polymorphism of PRNP gene at codon 129 does not differ from healthy European populations. Also codon 219 is monomorphic for the Glu allele both in Serbian population and other European populations. On the contrary, in Serbian population we did not detect any deletions or insertions in octapeptide repeat region, whereas deletions were detected in other European populations

Duchenne's/Becker's muscular dystrophy: Analysis of genotype-feno-type correlation in 28 patients

Duchenne's and Becker's muscular dystrophy (DMD & BMD) is a X linked disease caused by mutations in the dystrophic gene. DMD is the malign form of the disease, which significantly shortens the lifetime of the patient, while BMD has late onset with slow progression. Sixty five percent of DMD and BMD cases are caused by deletion of one or more exons in the dystrophic gene, while duplications cause these diseases in 6 to 7% of the cases. There are two hot spots for deletions and duplications. These are exons in the proximal part of the gene (3rd to 18th) and exons of a distal part of the gene (45th to 52nd). The remaining 30% of DMD and BMD cases are caused by point mutations, small deletions or inversions in the dystrophic gene. The correlation between School of Medicine, University of Belgrade, Belgrade the severity of the disease and the position of deletion shows that most of the out of frame deletions cause DMD phenotype, while in frame deletions result in BMD pheno-type. We report on the results of 28 non-related DMD and BMD patients. In 57% of cases deletions were detected and all were found in the distal hot spot of the gene. These results suggest that in most of the cases, out of frame deletions produce DMD phenotype while in frame deletions result in BMD phenotype. This is in compliance with data from literature

Identification of a broad spectrum of mammalian and avian species using the short fragment of the mitochondrially encoded cytochrome b gene.

Mitochondrial DNA (mtDNA), especially the gene for cytochrome b (MT-CYB), has been found to be highly informative for species identification. In this study, we present the results of the analysis of a 127 bp long fragment of MT-CYB, amplified using universal primers, variable enough to be used for species identification and discrimination, even in highly degraded animal samples. The total number of analyzed species in this study was 30, including 17 mammalian and 13 bird species. Using a newly created primer pair, we successfully amplified and sequenced the target sequence in almost all tested species. The amplification was incomplete in just two species, and as a result, partial, but still variable sequences, were obtained. Using the target fragment we successfully identified all tested samples. Initial results suggested that the intraspecies genetic diversity of the target region, in all tested species, was low - from 0 to 4.72%. The interspecies genetic diversity of the target region, crucial for successful discrimination, showed relatively high diversity, ranging from 8.36% to 42.52%. Given its short length, the target region should be used for species determination, particularly in samples that are degraded or are low in DNA quantity