Automated amplification and sequencing of human mitochondrial DNA

Lineage enforcement by inductive mesenchyme on adult epithelial stem cells across developmental germ layers

During development, cell differentiation is accompanied by the progressive loss of pluripotent gene expression and developmental potential, although de-differentiation in specialized cells can be induced by reprogramming strategies, indicating that transdifferentiation potential is retained in adult cells. The stromal niche provides differentiating cues to epithelial stem cells (SCs), but current evidence is restricted to tissue types within the same developmental germ layer lineage. Anticipating the use of adult SCs for tissue regeneration, we examined if stroma can enforce lineage commitment across germ layer boundaries and promote transdifferentiation of adult epithelial SCs. Here, we report tissue-specific mesenchyme instructing epithelial cells from a different germ layer origin to express dual phenotypes. Prostatic stroma induced mammary epithelia (or enriched Lin(-)CD29(HI)CD24(+/MOD) mammary SCs) to generate glandular epithelia expressing both prostatic and mammary markers such as steroid hormone receptors and transcription factors including Foxa1, Nkx3.1, and GATA-3. Array data implicated Hh and Wnt pathways in mediating stromal-epithelial interactions (validated by increased Cyclin D1 expression). Other recombinants of prostatic mesenchyme and skin epithelia, or preputial gland mesenchyme and bladder or esophageal epithelia, showed foci expressing new markers adjacent to the original epithelial differentiation (e.g., sebaceous cells within bladder urothelium), confirming altered lineage specification induced by stroma and evidence of cross-germ layer transdifferentiation. Thus, stromal cell niche is critical in maintaining (or redirecting) differentiation in adult epithelia. In order to use adult epithelial SCs in regenerative medicine, we must additionally regulate their intrinsic properties to prevent (or enable) transdifferentiation in specified SC niches.

Contrasting effects of in vitro fertilization and nuclear transfer on the expression of mtDNA replication factors

Mitochondrial DNA (mtDNA) is normally only inherited through the oocyte. However, nuclear transfer (NT), the fusion of a donor cell with an enucleated oocyte, can transmit both donor cell and recipient oocyte mtDNA. mtDNA replication is under the control of nuclear-encoded replication factors, such as polymerase gamma (POLG) and mitochondrial transcription factor A (TFAM). These are first expressed during late preimplantation embryo development. To account for the persistence of donor cell mtDNA, even when introduced at residual levels (mtDNA(R)), we hypothesized that POLG and TFAM would be upregulated in intra- and interspecific (ovine-ovine) and intergeneric (caprine-ovine) NT embryos when compared to in vitro fertilized (IVF) embryos. For the intra- and interspecific crosses, PolGA (catalytic subunit), PolGB (accessory subunit), and TFAM mRNA were expressed at the 2-cell stage in both nondepleted (mtDNA(+)) and mtDNA(R) embryos with protein being expressed up to the 16-cell stage for POLGA and TFAM. However, at the 16-cell stage, there was significantly more PolGA expression in the mtDNA(R) embryos compared to their mtDNA(+) counterparts. Expression for all three genes first matched IVF embryos at the blastocyst stage. In the intergeneric model, POLG was upregulated during preimplantation development. Although these embryos did not persist further than the 16+-cell stage, significantly more mtDNA(R) embryos reached this stage. However, the vast majority of these embryos were homoplasmic for recipient oocyte mtDNA. The upreglation in mtDNA replication factors was most likely due to the donor cells still expressing these factors prior to NT.

Mitochondrial D-loop (CA)n repeat length heteroplasmy: frequency in a German population sample and inheritance studies in two pedigrees

Sequence analysis of the human mitochondrial genome (mtDNA) has proven to be a valuable tool in forensic identity testing and the analysis of crime scene stains. In contrast to the very expensive sequencing technique, typing of different length variants can greatly facilitate screening of a large number of traces for their relevance during casework. Within the mitochondrial control region, a dinucleotide (CA)( n ) repeat locus is present. To assess the discrimination power of this marker, we have determined (CA)( n ) allele distribution and the frequency of heteroplasmy in a population sample of 2,458 Germans. The inclination to develop heteroplasmic mixtures (CA)( n )/(CA)( n-1) was positively correlated with the number of CA repeats in the mtDNA. In addition, we have studied the inheritance patterns of (CA)( n ) repeat sequence heteroplasmy in two pedigrees. In one pedigree, we also found a length heteroplasmy in the homopolymeric C-tract (nt 303-309). Our data show stable inheritance of heteroplasmy within the homopolymeric C-stretch, but rather unstable inheritance regarding the (CA)( n ) repeat locus.

Base composition analysis of human mitochondrial DNA using electrospray ionization mass spectrometry: a novel tool for the identification and differentiation of humans

In traditional approaches, mitochondrial DNA (mtDNA) variation is exploited for forensic identity testing by sequencing the two hypervariable regions of the human mtDNA control region. To reduce time and labor, single nucleotide polymorphism (SNP) assays are being sought to possibly replace sequencing. However, most SNP assays capture only a portion of the total variation within the desired regions, require a priori knowledge of the position of the SNP in the genome, and are generally not quantitative. Furthermore, with mtDNA, the clustering of SNPs complicates the design of SNP extension primers or hybridization probes. This article describes an automated electrospray ionization mass spectrometry method that can detect a number of clustered SNPs within an amplicon without a priori knowledge of specific SNP positions and can do so quantitatively. With this technique, the base composition of a PCR amplicon, less than 140 nucleotides in length, can be calculated. The difference in base composition between two samples indicates the presence of an SNP. Therefore, no post-PCR analytical construct needs to be developed to assess variation within a fragment. Of the 2754 different mtDNA sequences in the public forensic mtDNA database, nearly 90% could be resolved by the assay. The mass spectrometer is well suited to characterize and quantitate heteroplasmic samples or those containing mixtures. This makes possible the interpretation of mtDNA mixtures (as well as mixtures when assaying other SNPs). This assay can be expanded to assess genetic variation in the coding region of the mtDNA genome and can be automated to facilitate analysis of a large number of samples such as those encountered after a mass disaster.

FORENSICS ANDMITOCHONDRIALDNA: Applications, Debates, and Foundations

Debate on the validity and reliability of scientific methods often arises in the courtroom. When the government (i.e., the prosecution) is the proponent of evidence, the defense is obliged to challenge its admissibility. Regardless, those who seek to use DNA typing methodologies to analyze forensic biological evidence have a responsibility to understand the technology and its applications so a proper foundation(s) for its use can be laid. Mitochondrial DNA (mtDNA), an extranuclear genome, has certain features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. mtDNA typing has become routine in forensic biology and is used to analyze old bones, teeth, hair shafts, and other biological samples where nuclear DNA content is low. To evaluate results obtained by sequencing the two hypervariable regions of the control region of the human mtDNA genome, one must consider the genetically related issues of nomenclature, reference population databases, heteroplasmy, paternal leakage, recombination, and, of course, interpretation of results. We describe the approaches, the impact some issues may have on interpretation of mtDNA analyses, and some issues raised in the courtroom.

Personal identification from human remains by mitochondrial DNA sequencing

The authors report four cases in which severely damaged human remains were identified by mitochondrial DNA (mtDNA) sequencing. Degraded DNA was extracted from highly adipoceratous tissues using the phenol-chloroform method and polymerase chain reaction amplified for sequencing of two hypervariable regions, hypervariable region 1 and hypervariable region 2, of mitochondrial DNA. They also sequenced these regions of blood samples that were obtained from the presumptive mother or sister of the human remains. The sequencing results were compared with each other and with the Anderson's sequence. It was concluded from the sequence data that a lower part of a body in case 1 and some organs in case 2 were from the same woman, and a human head in case 3 and a female body in case 4 were from the relative of a presumptive mother and a sister, respectively.

A new improved method for extraction of DNA from teeth for the analysis of hypervariable loci

A new method for better recovery of DNA suitable for amplification of hypervariable loci from fragments of teeth, consisting of two steps-scraping and aspiration, and extensive decalcification-is reported. Higher yields of high molecular weight DNA were obtained from the root, pulp, and crown of all kinds of 120 teeth, irrespective of gender, age, and source of teeth. HLA DQA1, 5 poly markers (LDLR, GYPA, HBGG, D7S8, and Gc), and other 12 short tandem repeat loci (HPRTB, F13B, LPL, D13S317, D7S820, D5S818, D21S11, D18S51, FGA, D8S1179, D3S1358, and vWA) could be successfully amplified and typed from recovered DNA.

Efficiency of forensic mtDNA analysis. Case examples demonstrating the identification of traces

The paper presents results of forensic mitochondrial DNA analyses which were aimed at typing the traces caused by touching or abrasion of skin cells. Five cases of strangulation tool investigation are summarised. Two cases of homicide could be cleared up by identifying the mtDNA of both the victim and the suspect on cables which had obviously been used as strangulation tools. In eight of 10 cases, weapons could be reliably assigned to their users. The mtDNA of the users could be even detected on cartridges after firing. In one case, evidence of a suicide could be provided by means of mtDNA sequencing of the wiping traces on a suicide note.

Mitochondrial DNA in the Central European population. Human identification with the help of the forensic mt-DNA D-loop-base database

Sequencing of mtDNA is an advanced method for the individualisation of traces. Disadvantages of this method are expensive and time-consuming analysis and evaluation procedures as well as the necessary stock of population-genetic data which is still insufficient. Central European institutes of forensic medicine from Germany, Austria, and Switzerland have been working together since the beginning of 1998 to establish a mtDNA database. The aim is to build up a large stock of forensically established data and provide population-genetic data for frequency investigations, which will serve as a basis for expert opinions and scientific research. Good data quality is ensured by using original sequences only. Ring tests, which have been conducted to enhance analytical reliability, revealed a high correspondence rate of the analytical results obtained by the individual member institutes. Today 1410 sequences are available for comparison, of which 1285 sequences in the HV1 and HV2 regions cover the full ranges from 16051 to 16365 and from 73 to 340 (according to Anderson). The major part is formed by Central European sequences comprising 1256 data sets from Germany, Austria, and Switzerland. Today the database contains sequences from a total of 12 European, six African and three Asian countries including 100 sequences from Japan. This paper is aimed at discussing the individualisation potentials of mtDNA as well as the possibilities and limits of ethnic differentiation by means of pairwise sequence differences on the basis of the data stock available.

A study on polymerase chain reaction-based HLA DQ alpha locus in Elaziğ, Turkey

The polymerase chain reaction (PCR) was used for genetic characterization of 45 samples taken from the city of Elaziğ in Turkey. The polymorphism at the human leukocyte antigen DQalpha locus was detected. Allele and genotype frequencies were determined for unrelated individuals at this locus. Laboratory analyses were done by PCR amplification of DNA. Hybridization to allele specific oligonucleotide probes was performed using a reversed dot-blot typing method. The collected genotype and allele frequencies have been tested, and a comparison was made with other population surveys of this locus. Allele frequencies ranged from 3.3% (allele 1.3) to 36.7% (allele 4), with a discrimination power of 0.92. No deviation was seen from Hardy-Weinberg equilibrium in the findings.

Forensic applications of mitochondrial DNA

Human mitochondrial DNA has become a useful tool in forensic investigations. Its polymorphic nature and maternal inheritance are characteristics that have, combined with its sequence information, enabled investigators to identify missing persons, war casualties and individuals involved in mass disasters and criminal cases. Various screening procedures have been developed to reduce the need to sequence samples that do not match, but DNA-sequence information is still necessary to verify a match. Even though several challenges remain before mitochondrial-DNA-sequence information can be used unambiguously, comparative mitochondrial-DNA-sequence analysis appears to be a reliable and powerful means for human identification.

Rapid mitochondrial DNA typing using restriction enzyme digestion of polymerase chain reaction amplicons followed by capillary electrophoresis separation with laser-induced fluorescence detection

The polymorphic control region of mitochondrial DNA (mtDNA) is becoming more commonly used in forensic applications to differentiate among individuals in a population. Two hypervariable regions (HV1 and HV2) are often sequenced following amplification of the mtDNA via the polymerase chain reaction (PCR). More rapid screening assays would reduce both the effort and the expense of comparing two samples. A methodology has been developed that first uses restriction endonuclease digestion of the PCR-amplified mtDNA using RsaI and MnlI and then capillary electrophoresis (CE) to separate and size the PCR-RFLP fragments. This rapid procedure offers an alternative method for screening of polymorphisms in amplified mtDNA samples. In addition, the presence of a T-->C transition at position 16189, which gives rise to the so-called "C-stretch" in HV1, may be predicted from the presence of nonspecific PCR products in the CE results.

Mitochondrial D-loop 3' (CA)n repeat polymorphism: optimization of analysis and population data

We report a dinucleotide repeat polymorphism in the 3' area of the mitochondrial control region. The fragments obtained using a new primer set could be reliably separated by polyacrylamide gel electrophoresis (PAGE) using nondenaturing gels. A total of five alleles [(CA)3 to (CA)7] were detected on silver-stained gels. The 90 bp product corresponds to allele 5. Samples from one African and three European populations were characterized. Significant differences could be demonstrated as to the incidence of single alleles and allele distributions in different populations. These differences were found between the three European and one African Bantu population. For specific forensic questions the mitochondrial CA repeat is well suited. Gene diversities in populations of Germany, Hungary, the Russian Federation and Cameroon were 0.36, 0.40, 0.34, 0.52, respectively.

Sequence variation of mitochondrial DNA control region in Koreans

The sequencing data for two mtDNA segments in control region I and II, 385 and 341 nucleotides long, respectively, for 306 unrelated Koreans are presented. In regions I and II, 139 and 58 polymorphic sites, respectively, were noted. These were distributed evenly along the control region, though the frequency of each site was variable. Nucleotide substitution rather than insertion/deletion was the prevalent pattern of variation. A total of 265 different mtDNA lineages in region I and 154 in region II were revealed. This result represents a substantial level of polymorphism in a defined population, and presents the possibility that mtDNA polymorphism could be used as an individual identification marker, especially when nuclear DNA is not available. In view of the complex pattern of variation, meticulous test-sequencing is thought to be more appropriate than RFLP analysis using restriction endonuclease or hybridization using an SSO probe. Racial differences with genealogical usage are also described.

Rapid detection of sequence polymorphisms in the human mitochondrial DNA control region by polymerase chain reaction and single-strand conformation analysis in mutation detection enhancement gels

The article describes a rapid approach for the detection of sequence polymorphisms in the mitochondrial (mt)DNA control region that involves enzymatic amplification of each entire mtDNA control region (HV1 and HV2) and the subsequent analysis of the PCR products by single-strand conformation analysis (SSCA) in mutation detection enhancement (MDE) gels, followed by silver stain detection. HV1 and HV2 SSC reference ladders were developed to standardize the classification of the different mtDNA types. Twenty-five mtDNA types were observed among the 45 Spanish individuals analyzed: 11 types were observed in the HV1 region as compared with 10 types in the HV2 region. This mutation scanning strategy could be a promising method of potential use not only in forensic genetics but also in population and evolutionary studies.

Ancient, highly polymorphic human major histocompatibility complex DQA1 intron sequences

A 438 basepair intron 1 sequence adjacent to exon 2 in the human major histocompatibility complex DQA1 gene defined 16 allelic variants in 69 individuals from wide ethnic backgrounds. In contrast, the most variable coding region spanned by the 247 basepair exon 2 defined 11 allelic variants. Our phylogenetic human intron 1 tree derived by the Bootstrap algorithm reflects the same relative allelic relationships as the reported DQA1 exon 2 tree [Gyllensten and Erlich, Hum Immunol 36:1-10, 1989]. Thus 3' DQA1 intron 1 and exon 2 have cosegregated since divergence of the human races. Comparison of human alleles to a Rhesus monkey DQA1 first intron sequence found only 10 nucleotide substitutions unique to Rhesus, with the other 428 positions (98%) found in at least one human allele. This high degree of homology reflects the evolutionary stability of intron sequences since these two species diverged over 20 million years ago. Because more intron 1 alleles exist than exon 2 alleles, these polymorphic introns can be used to improve tissue typing for transplantation, paternity testing, and forensics and to derive more complete phylogenetic trees. These results suggest that introns represent a previously underutilized polymorphic resource.

Investigation of the STR locus HUMTH01 using PCR and two electrophoresis formats: UK and Galician Caucasian population surveys and usefulness in paternity investigations

Two hundred unrelated Caucasians from the UK and 210 from Galicia (NW Spain) have been genotyped for the HUMTH01 locus using polymerase chain reaction (PCR) amplification followed by high sieving agarose electrophoresis (UK samples) and polyacrylamide electrophoresis (Galician samples). Allele and genotype frequencies obtained from both populations were in close agreement to those seen by other workers and chi 2 tests of the two populations showed that both were in Hardy-Weinberg equilibrium. The potential usefulness of HUMTH01 in paternity investigations was analysed by constructing, within each population, false family trios, each with a non-father, in order to estimate the actual exclusion rate. The observed rate of exclusion was in close agreement with the expected rate for both populations. Examination of the mother-child pairs in the false families showed a common allele in every case and no evidence of mutation or non-Mendelian inheritance was observed. The HUMTH01 locus shows an informative polymorphism and the production and analysis of population databases is easily achieved. The use of PCR followed by electrophoresis in either gel format appears to provide a quick and straightforward method for investigating the HUMTH01 locus.

Identification of the remains of the Romanov family by DNA analysis

Nine skeletons found in a shallow grave in Ekaterinburg, Russia, in July 1991, were tentatively identified by Russian forensic authorities as the remains of the last Tsar, Tsarina, three of their five children, the Royal Physician and three servants. We have performed DNA based sex testing and short tandem repeat (STR) analysis and confirm that a family group was present in the grave. Analysis of mitochondrial (mt) DNA reveals an exact sequence match between the putative Tsarina and the three children with a living maternal relative. Amplified mtDNA extracted from the remains of the putative Tsar has been cloned to demonstrate heteroplasmy at a single base within the mtDNA control region. One of these sequences matches two living maternal relatives of the Tsar. We conclude that the DNA evidence supports the hypothesis that the remains are those of the Romanov family.

The application of mitochondrial DNA typing to the study of white Caucasian genetic identification

Mitochondrial DNA (mtDNA) from 100 unrelated British White Caucasians was extracted, amplified and directly sequenced. Sequences of approximately 800 nucleotides were obtained from 2 hypervariable segments within the non-coding region of the mitochondrial genome. A total of 91 different sequences were observed with an average nucleotide diversity of 1.1%. The most diverse pair of sequences differed at 3.6% of their nucleotide (nt) sites. Comparison to a consensus reference sequence showed that each region was polymorphic to a similar extent. Different methods of genetic analysis were used to examine the variation in each region, including pairwise comparisons, which demonstrated that although the data did not fit a Poisson distribution, the fit was closer to a Negative Binomial distribution.

Identification of human remains by amplification and automated sequencing of mitochondrial DNA

The highly decomposed remains of a corpse were identified by the amplification and direct sequencing of mitochondrial (mt) DNA. Degraded DNA was extracted from bone fragments and a necrotic skin sample and amplified at 2 hypervariable segments within the mitochondrial non-coding region using 2 rounds of nested PCR. Both strands of the amplified regions were sequenced and compared with each other to ensure fidelity of the data. Sequences from the bone and skin were found to be identical and matched data generated from a blood sample provided by a presumptive sister of the deceased. Thus, this evidence was consistent with the sister and the deceased being related.

Characterisation of HLA DQ alpha for forensic purposes. Allele and genotype frequencies in British Caucasian, Afro-Caribbean and Asian populations

Allele and genotype frequencies for British Caucasian, Afro-Caribbean and Asian populations were determined for a total of over 600 unrelated individuals at the HLA-DQ alpha locus. These were analysed by polymerase chain reaction amplification of the DNA followed by hybridisation to allele specific oligonucleotide probes in a reversed dot-blot test. Six different alleles were detected and the allele distributions for the 3 populations analysed displayed significant differences. However, the British Caucasian genotypes were statistically very similar to previously published data from US Caucasians as were British Afro-Caribbean genotype frequencies with US Black data. In Caucasians the allele frequencies ranged from 5.2% to 26.9% with a power of discrimination of 0.93. DQ alpha genotype frequencies of Caucasian and Afro-Caribbean populations do not deviate from Hardy-Weinberg equilibrium. However, the Asian data displayed significant deviation due to excess homozygotes.

Advances in DNA sequencing technology

Efforts to map and sequence the genomes of the human and other species have stimulated efforts to improve the technology required for these endeavors. During the last year, these efforts have produced substantial advances in DNA template preparation, sequencing chemistry, and gel analysis.