Publications by authors named "Helena Suryadi"

9 Publications

  • Page 1 of 1

Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis).

BMC Res Notes 2021 Mar 26;14(1):119. Epub 2021 Mar 26.

Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.

Objective: The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling.

Results: Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; H = 0.30). These were sufficient to distinguish among individuals (P < 0.0001), and to distinguish among siblings (P < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.
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http://dx.doi.org/10.1186/s13104-021-05522-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995689PMC
March 2021

Allele frequency data for 15 autosomal STR loci in eight Indonesian subpopulations.

Forensic Sci Int Genet 2016 Jan 3;20:45-52. Epub 2015 Oct 3.

National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia.

Evolutionary and cultural history can affect the genetic characteristics of a population and influences the frequency of different variants at a particular genetic marker (allele frequency). These characteristics directly influence the strength of forensic DNA evidence and make the availability of suitable allele frequency information for every discrete country or jurisdiction highly relevant. Population sub-structure within Indonesia has not been well characterised but should be expected given the complex geographical, linguistic and cultural architecture of the Indonesian population. Here we use forensic short tandem repeat (STR) markers to identify a number of distinct genetic subpopulations within Indonesia and calculate appropriate population sub-structure correction factors. This data represents the most comprehensive investigation of population sub-structure within Indonesia to date using these markers. The results demonstrate that significant sub-structure is present within the Indonesian population and must be accounted for using island specific allele frequencies and corresponding sub-structure correction factors in the calculation of forensic DNA match statistics.
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http://dx.doi.org/10.1016/j.fsigen.2015.09.014DOI Listing
January 2016

Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations.

BMC Genomics 2015 Mar 17;16:191. Epub 2015 Mar 17.

Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.

Background: Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma'anyan. To test for a genetic link between Malagasy and these linguistically related Indonesian populations, we studied the Ma'anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar.

Result: A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands.

Conclusion: Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma'anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized.
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http://dx.doi.org/10.1186/s12864-015-1394-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373124PMC
March 2015

Mapping human genetic diversity in Asia.

Science 2009 Dec;326(5959):1541-5

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.
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http://dx.doi.org/10.1126/science.1177074DOI Listing
December 2009

Mapping human genetic diversity in Asia.

Science 2009 Dec;326(5959):1541-5

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.
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http://dx.doi.org/10.1126/science.1177074DOI Listing
December 2009

Mitochondrial genome and susceptibility to diabetes mellitus.

Adv Exp Med Biol 2003 ;531:19-36

Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, Indonesia.

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http://dx.doi.org/10.1007/978-1-4615-0059-9_2DOI Listing
September 2003

Human genome diversity and disease on the island Southeast Asia.

Adv Exp Med Biol 2003 ;531:3-18

Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta, Indonesia.

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http://dx.doi.org/10.1007/978-1-4615-0059-9_1DOI Listing
September 2003

Asian-specific mtDNA backgrounds associated with the primary G11778A mutation of Leber's hereditary optic neuropathy.

J Hum Genet 2002 ;47(11):594-604

Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia.

We studied 19 patients of Southeast Asian (SEA) ethnic ancestry with Leber's hereditary optic neuropathy (LHON) to investigate the mtDNA haplotypes associated with the primary mutation(s). Eighteen patients carried a mitochondrial DNA (mtDNA) G11778A mutation (Arg340His in the respiratory complex I ND4 subunit), while one had a T14484C mutation (Met64Val in the ND6 subunit). One patient had a class II LHON mtDNA mutation, G3316A. Sequencing data of the ND genes showed many single-nucleotide polymorphisms (62 SNPs in 17 individuals; 10 LHON patients and 7 normal controls) not previously reported in Europeans or Japanese. The SEA G11778A LHON mutation was associated mostly with two mtDNA haplogroups, M (47%) and a novel lineage, characterized by the gain of a 10394 DdeI site but absence of the 10397 AluI site, designated BM (37%). A significant association was observed between one SNP, A10398G, resulting in a Thr114Ala substitution in the ND3 subunit, and the primary LHON mutation. This SNP also characterizes haplogroup J, with which the European LHON 11778 and 14484 mutations show preferential association. The combination of A10398G and other SNPs, specific for the haplogroups J, M, or BM, might act synergistically to increase the penetrance of the LHON mutations, thus allowing their detection.
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http://dx.doi.org/10.1007/s100380200091DOI Listing
January 2003

Nuclear mitochondrial interplay in the modulation of the homopolymeric tract length heteroplasmy in the control (D-loop) region of the mitochondrial DNA.

Hum Genet 2002 May 4;110(5):402-11. Epub 2002 Apr 4.

Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, Jakarta 10430, Indonesia.

We have studied the genetic characteristics of a homopolymeric tract length heteroplasmy associated with the 16189C variant in the mtDNA D-loop control region to identify the factor(s) involved in the generation of the length heteroplasmy. The relative proportion of the various lengths of the polycytosines (i.e., the pattern of the length heteroplasmy) is maintained in an individual, and previous evidence shows that it is regenerated de novo following cell divisions. The pattern is maintained in maternally related individuals, suggestive of mtDNA determinants. Of the 38 individuals with the 16189C variant studied, 39% were found to exhibit the (16180)AAACCCCCCCCCCC(16193) variant associated with A16183C polymorphism [(11C)-group], while 53% showed the (16180)AACCCCCCCCCCCC(16193) variant associated with a further A16182C polymorphism [(12C)-group]. Haplotype analysis of the mtDNA revealed a specific association of the longer mean length of the poly[C] in the (12C)-group with haplogroup B. A similar association was also observed in the (11C)-group, but with a novel haplogroup. Cybrid constructions revealed that the involvement of nuclear factor(s) in the generation of the length heteroplasmy is prominent in homopolymeric tract of eight cytosines. The nuclearly coded factor(s) is/are presumably related to the fidelity of the nuclearly coded components of the mitochondrial DNA replication machinery.
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http://dx.doi.org/10.1007/s00439-002-0717-3DOI Listing
May 2002
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