Anderson's Sequence Research Articles

Forensic Genetic Analysis of Mitochondrial DNA Hypervariable Region III Sequences in Muslims from South India

The absence of recombination, high rate of mutation, and maternal inheritance of the mitochondrial DNA (mtDNA) genome makes it a valuable tool in many fields including evolutionary anthropology, genetic genealogy, population history, and forensic science. The mtDNA genome can be separated into two parts: a large coding region and a smaller fragment called the control region or non-coding region that generally referred to as displacement loop (D loop). The mtDNA D-loop region was highly polymorphic and has proven a precious marker in forensic identification. The study aims to examine and suggests polymorphism of the HVRIII region as a power marker along with HVRI and HVRII in forensic investigations. Within the control region of the mtDNA genome, the sequences of hypervariable region III (HVR III) (nucleotide position 438-574) were obtained from 60 unrelated Muslims of Shrirangapattana town, located in Karnataka state of South India. The complete mtDNA control region was amplified and sequenced by the Sanger sequencing method. The study provided the identification of 18 different haplotypes and 17 polymorphic nucleotide positions. The most common haplotype (H.18) was consistent with the Anderson sequence which occurred fourteen times. The distribution of nucleotide substitutions, insertions, and deletions was computed and determined that transitions made up the majority of the variations (58%) in this region. The genetic diversity was estimated at 0.89939 and the random match probability at 0.1155. The power of discrimination was found to be 0.8844 and the rest of the statistical parameters such as the mean of pair-wise differences and nucleotide diversity were established as 2.255932 ± 1.25884 and 0.010071± 0.00623, respectively. Consequently, the discovery of high genetic, haplotype, and nucleotide diversity, and high power of discrimination impart the use of hypervariable region III (HVR III) as an important marker in forensic investigations.

Volcanic reconstruction of the Paleoproterozoic Stroud Breccia: Understanding the transition from a primitive to mature arc and its impact on VMS ore-formation, Snow Lake, Manitoba, Canada

The Stroud Breccia is a ≤400 m thick package of dominantly felsic volcaniclastic rocks within the Paleoproterozoic Snow Lake arc assemblage. It stratigraphically overlies the ore-interval for the Anderson, Stall and Rod volcanogenic massive sulfide (VMS) deposits at Snow Lake, Manitoba, Canada and occupies the stratigraphic interval between the underlying primitive arc Anderson sequence and the overlying mature arc Chisel sequence.The Stroud Breccia is interpreted to be a product of subaqueous pyroclastic and effusive, dominantly rhyolitic, volcanism, and concomitant subsidence. It consists of felsic tuff to lapilli-tuff, crystal-rich felsic tuff, felsic lapillistone, felsic tuff breccia, mafic tuff to lapilli-tuff, heterolithic tuff breccia to breccia and rhyolite. The finer felsic volcaniclastic units are characterised by angular or broken quartz crystals, angular lithic rhyolite lapilli, and pumice. Fine ash, broken crystals and pumice suggest they were deposited by eruption-fed density currents associated with a phreatomagmatic eruption. The coarser felsic volcaniclastic units are characterized by blocks of strongly quartz-feldspar porphyritic rhyolite and pumice and are interpreted to have been deposited during the reworking of pyroclastic debris flow deposits on the seafloor during mass wasting events at fault scarps. Planar and cross laminations, graded beds and bomb sag structures suggest the mafic tuff to lapilli-tuff unit was deposited by a combination of subaqueous eruption-fed density currents and eruption driven ballistically emplaced ejecta, likely through subaqueous tephra jetting.Lithofacies analyses, and geochemistry has allowed comparison between the felsic volcanic rocks of the Stroud Breccia and those that host the Anderson, Stall and Rod VMS deposits. Detailed mapping has led to the identification of synvolcanic faults, defining basins and volcanic vents, that indicate that the process of incipient rifting of the Anderson sequence primitive arc continued during emplacement of the Stroud Breccia. These structures also define magma and fluid pathways critical in controlling the formation of the Anderson VMS deposits, meaning they represent deep-seated and long-lived structures that can be used as vectors to mineralization at depth.

Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy

Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy.The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.

Five coding region polymorphism of mitochondrial DNA in Chinese Han population of Yanbian area

To investigate the mitochondrial DNA (mtDNA) five coding region sequence polymorphisms encompassing positions nt3954-4506, nt5218-5974, nt7942-8711, nt10296-10653, and nt14496-14867 in Chinese Han population of Yanbian area, Jilin province. Polymerase chain reaction (PCR) and direct sequencing method were used to detect the haplotype distribution of mtDNA coding region in 200 unrelated Chinese Han individuals. One hundred and ten haplotypes were observed in the 200 individuals. The gene diversity was 0.9879 and the random match probability was 0.0171. Compared with the Anderson's sequence,81 nucleotide variants were obtained,of which 66 were previously registered in MITOMAP,and 15 were novel. The obtained data suggest that these sequence polymorphisms are valuable genetic markers for personal identification when added to mtDAN control region investigation, and thus could be used as basic data for the forensic application in Chinese Han population.

Mitochondrial DNA control region database in Banco Nacional de Datos Genéticos, Argentina

To analyze the distribution of different haplotypes of mitochondrial control region DNA in a large sample of argentine population who assisted to the Banco Nacional de Datos Genéticos (BNDG) looking for their identity in cases of civil state suppression during the dictatorial government (1976–1983). A total of 1168 unrelated argentine individuals who assisted to the BNDG were sampled for the analysis. Mitochondrial DNA Control Region sequences were determined for both hypervariable regions 1 (HV1) and 2 (HV2). Blood samples were used as the DNA source. The amplification for both hypervariable regions was performed in a Perkin Elmer 9700 thermal cycler. The cycle sequencing was performed using the BigDye ® Terminator v 1.1 Cycle Sequencing Kit (Applied Biosystems) and automated sequencing was performed in an ABIPRISM ® 3100 Genetic Analyzer (Applied Biosystems). Analysis of mitochondrial DNA sequencing data was performed by manual method. The hypervariable region 1 (HV1) was analyzed between positions 16023 and 16428 and the hypervariable region 2 (HV2) between 50 and 480 according to the Anderson Sequence. To analyze these results a database was created and statistical parameters were calculated. From 1168 haplotypes analyzed, 794 were unique. Haplotype frequencies were estimated by haplotype counting. Values of Genetic Identity ( P) and Genetic Diversity ( h) were calculated, being 3.3939 × 10 −3 and 0.9974 respectively. This Mitochondrial Control Region DNA database provides useful information for genetic profiles comparison and maternal lineage determination in our lab.

Mitochondrial DNA coding region 3954-4506 polymorphism in Korean Chinese population

To investigate the sequence polymorphism of mtDNA coding region encompassing nt3954-4506 in the Korean Chinese population of Yanbian area. Polymerase chain reaction (PCR) and direct sequencing method were used to detect the haplotype distribution of mtDNA coding region in 198 Korean Chinese individuals. Twenty-one haplotypes were observed in the 198 unrelated individuals. The genetic diversity was 0.5906 and the random match probability was 0.4124. Compared with the Andersonos sequence, 19 nucleotide variants were found, of which 14 were previously registered in MITOMAP, and 5 were novel. The obtained data suggest that these sequence polymorphisms are valuable genetic markers for personal identification when combined with mtDAN control region investigation, thus could be used as basic data for the forensic application in Korean Chinese population.

Sequence polymorphism of mtDNA HVR Ⅰ and HVR Ⅱ of Oroqen ethnic group in Inner Mongolia

Venous blood samples from 50 unrelated Oroqen individuals living in Inner Mongolia were collected and their mtDNA HVR I and HVR II sequences were detected by using ABI PRISM377 sequencers. The number of polymorphic loci, haplotype, haplotype frequence, average nucleotide variability and other polymorphic parameters were calculated. Based on Oroqen mtDNA sequence data obtained in our experiments and published data, genetic distance between Oroqen ethnic group and other populations were computered by Nei's measure. Phylogenetic tree was constructed by Neighbor Joining method. Comparing with Anderson sequence, 52 polymorphic loci in HVR I and 24 loci in HVR II were found in Oroqen mtDNA sequence, 38 and 27 haplotypes were defined herewith. Haplotype diversity and average nucleotide variability were 0.964+/-0.018 and 7.379 in HVR I, 0.929+/-0.019 and 2.408 in HVR II respectively. Fst and dA genetic distance between 12 populations were calculated based on HVR I sequence, and their relative coefficients were 0.993(P < 0.01). A phylogenetic tree was constructed based on genetic distances and included Oroqen, Taiwan and South Han population in a clade, which indicated near genetic relation between them, and far relation with northern Han, Mongolian and other foreign populations. The genetic polymorphism of mtDNA HVR I and HVR II in Oroqen ethnic group has some specificities compared with that of other populations. These data provide a useful tool in forensic identification, population genetic study and other research fields.

Genetic polymorphism of mitochondrial DNA HVS-I and HVS-II of Chinese Tu ethnic minority group

We analyzed the two hypervariable segments HVS-I and HVS-II of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes. Comparing with Anderson sequence, 79 polymorphic loci in HVS-I and 40 in HVS-II were found in Chinese Tu ethnic minority group mtDNA sequences, and 90 and 64 haplotypes were then defined. Haplotype diversity and the mean pairwise differences were 0.9903±0.0013 and 5.7785 in HVS-I, and 0.9777±0.0013 and 3.5819 in HVS-II, respectively. By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-I, we defined some new types of sequence variations. We also compared the relationship between Tu population and other populations using mtDNA HVS-I sequences. According to Rst genetic distances, the phylogenetic tree showed that the Tu population, the Xi'an Han population, the Chinese Korean, and the Mongol ethnic group were in a clade. This indicated a close genetic relationship between them. There were far relations between the Tu population and other Chinese southern Han populations, Siberian, European, African, and other foreign populations. The results suggest that Tu population has a multi-origin and has also merged with other local populations.

Polymorphisms analysis of mitochondrial DNA in coding area

ObjectiveTo analyze mitochondrial DNA (mtDNA) polymorphisms in coding area and provide a theoretical basis to apply in Forensic Science. MethodsThe primers of 8162F/8483R and 13070F/13299R were designed according to the Anderson's sequence. Using PCR-sequencing method to detect polymorphisms of mtDNA nt8162–8483 and nt13070–13299. ResultsThe lengths of the amplicons were 322 bp and 230 bp, respectively. There were 24 mitochondrial haplotypes defined by 21 variable positions in both regions. The gene diversity was estimated at 75.11%, and the probability of two randomly selected individuals having identical mtDNA types was 25.64%. ConclusionsThe polymorphic sites within mtDNA coding area can be useful in combination with mtDNA control region in order to increase the discriminational power.

Population data of mitochondrial DNA region HVIII in 150 individuals from Bologna (Italy)

Mitochondrial DNA (mtDNA) sequence variations at the HVIII region in 150 unrelated Italian individuals from Bologna were analysed. A comparison of our sequence data with the Anderson sequence showed that nucleotide substitutions predominate over insertions and deletions. Among nucleotide substitutions the most frequent was a T–C transition.

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.

Sequence polymorphism of mitochondrial D-loop DNA in the Taiwanese Han population

In order to demonstrate the sequence diversity of mitochondrial D-loop DNA in the Taiwanese Han population, we established a database of 155 unrelated individuals. For each individual, the complete 980 bp DNA region from the 5′ end of HVI to 3′ end of HVII segment was sequenced. In these 155 sequence data, 149 different haplotypes were observed, amongst these haplotypes, 144 were unique, 4 were found in 2 individuals and 1 was found in 3 individuals. When compare to the Anderson sequence, 144 transitions, 24 transversions, 5 insertions and 5 deletions were found. Eight positions exhibited more than one polymorphic sequence, six exhibited two variants while two exhibited three variants. Over the 1024 bp that was analysed, pairwise differences between the sequences were 11.35±3.53 bp. The sequence and nucleotide diversity were 0.9994 and 0.0116, respectively. The probability of two individuals randomly matching over the entire control region was 0.007. The diversity in the mitochondrial D-loop indicates the value of this locus for casework within Taiwan.

A lifetime of retinal light exposure does not appear to increase mitochondrial mutations

Recently, there have been a number of reports of an accumulation of mutations in the mitochondrial (mt) genome with age. Such mutations may be due in part to the mt oxidative metabolic pathways which provide most of the cell's energy, but also generate free radicals. In addition, the mt genome in some tissues, such as the retina, may also accumulate mutations from the effects of ultraviolet light. To obtain information concerning the possible accumulation of retinal mt mutations with age, we cloned retinal mt DNA from a 71-year-old person. Thirty-two kilobases of sequence from 83 independently isolated clones representing two regions, a coding and a noncoding region, of the mt genome were obtained. Three polymorphisms between these sequences and the standard ‘Anderson sequence’ were discovered. Only one heteroplasmic mutation was found. These results confirm the low somatic mutation rate found in prior studies utilizing different types of human tissues. In addition, these results suggest that there is little if any accumulated damage to the mt DNA of the retina during normal aging.