Abdul Salam M. Sofro, Abdul Salam
Sekolah Pasca Sarjana Universitas YARSI Jakarta

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Pengembangan Metode In-House HLA-Typing Gen HLA Kelas I (HLA A, HLA B, dan HLA C) Menggunakan Next Generation Sequencing Illumina MiSeq Yuliwulandari, Rika; Prayuni, Kinasih; Kenconoviyati, Kenconoviyati; Susilowati, R. W.; M. Sofro, Abdul Salam
Majalah Kedokteran Bandung Vol 47, No 3 (2015)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (597.787 KB)

Abstract

Human leucocyte antigen (HLA) adalah protein penyaji antigen yang lokus genetiknya berada di kromosom 6p21 dengan ukuran sebesar 3,8 Mb dan berasosiasi dengan lebih dari 100 penyakit berbeda yang  kebanyakan merupakan penyakit autoimun. Proses HLA-typing menggunakan sekuensing Sanger masih memberikan ambiguitas terhadap determinasi alel, low-throughput, dan membutuhkan biaya besar untuk sampel dalam jumlah besar. Next generation sequencing (NGS) menjadi metode yang dapat mengatasi kelemahan sekuensing Sanger. MiSeq dari Illumina merupakan salah satu NGS yang digunakan untuk HLA-typing. MiSeq memberikan kemudahan preparasi dan fleksibilitas metode yang dapat dikembangkan sesuai dengan kebutuhan laboratorium penelitian. Penelitian dilakukan di Laboratorium Molekular Genetik, Laboratorium Terpadu Universitas YARSI pada empat orang mahasiswa Fakultas Kedokteran Universitas YARSI etnik Melayu selama periode Mei–Desember 2014. Hasil menunjukkan terdapat total 546 SNP heterozygous, 888 SNP homozygous, 25 insersi, dan 23 delesi dari keseluruhan 11 sampel amplikon dengan coverage 2.106,536x dengan 2x25 siklus pembacaan. Optimasi metode HLA-typing dapat dikatakan berhasil dengan mengombinasikan long-range PCR dan pemilihan ukuran library 300–600 bp. [MKB. 2015;47(3):152–159]Kata kunci: HLA Kelas I, MiSeq, next generation sequencingDevelopment of Class I HLA Gene In-House HLA-Typing Methods (HLA A, HLA B, and HLA C) using Next Generation Sequencing Illumina MiSeqAbstractHuman leukocyte antigen (HLA) is a 3.8 Mb protein presenting antigen whose genetic locus is located in chromosome 6p21 area and have association with more than 100 different diseases that are mostly autoimmune diseases. HLA-typing process using Sanger sequencing still  creates ambiguity in the  determination of  alleles, low-throughput, and costly as it requires a large quantity of sample. Next generation sequencing (NGS) is a method that can overcome the drawbacks of Sanger sequencing. MiSeq Illumina is one of the NGSs that are used for HLA-typing. This study was conducted at the Laboratory of Molecular, Universitas YARSI in a period from May to December 2014. MiSeq provides convenience and flexibility in the preparation methods that can be developed according to the needs of the research laboratory. The results showed that there were a total of 546 SNPs that were heterozygous, 888homozygous SNP, 25 insertions and 23 deletions from the overall 11 amplicon samples with an average coverage with 2x25 read length of  2,106,536x. Our protocol generates good result as we combined long PCR amplicon and size selection method to 300–600 bp fragment.  [MKB. 2015;47(3):152–159]Key words: HLA Class I, MiSeq, next generation sequencing DOI: 10.15395/mkb.v47n3.389
The density of collagen fiber in alveolus mandibular bone of rabbit after augmentation with powder demineralized bone matrix post incisivus extraction Tandelilin, Regina TC.; M. Sofro, Abdul Salam; Santoso, Al Supartinah; Soesatyo, Marsetyawan HNE; Asmara, Widya
Dental Journal (Majalah Kedokteran Gigi) Vol 39, No 2 (2006): (June 2006)
Publisher : Faculty of Dental Medicine, Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (225.688 KB) | DOI: 10.20473/j.djmkg.v39.i2.p43-47

Abstract

The bone defect due to tooth extraction contributes the most cases reported in the aspects of oral surgery. The defect can be preventively managed by adding powder bone matrix intended for augmentation which eventually induces the formation of new bones. This hard tissue wound healing is preceded by the presence of collagen fibers. The aim of this study was to determine the density of collagen fiber in the alveolus mandibular bone of rabbit which was augmented using powder demineralized bone matrix (DBM) post incisivus extraction. Twenty four male rabbits aged 2.5–3 months weighed 900–1,100 grams were randomly divided into two groups. The treated rabbits were augmented with DBM after the incisivus extraction on mandible. The mucosa was then sutured. On the other hand, the controlled rabbits received similar treatments with those of the treated rabbits except there was no augmentation of DBM. Decapitation of treated and controlled rabbits was made on day 5, 7, 10, and 14 days post surgery, each with three rabbits. Mandibles were cut, decalcified, and imbedded in paraffin block. The staining was done using Mallory. Significant differences in the density of collagen were noted on day 10 and 14 post surgery, indicating that powder demineralized bone matrix successfully induced the stimulation of collagen.
Pengembangan Metode In-House HLA-Typing Gen HLA Kelas I (HLA A, HLA B, dan HLA C) Menggunakan Next Generation Sequencing Illumina MiSeq Yuliwulandari, Rika; Prayuni, Kinasih; Kenconoviyati, Kenconoviyati; Susilowati, R. W.; M. Sofro, Abdul Salam
Majalah Kedokteran Bandung Vol 47, No 3 (2015)
Publisher : Faculty of Medicine, Universitas Padjadjaran

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (597.787 KB)

Abstract

Human leucocyte antigen (HLA) adalah protein penyaji antigen yang lokus genetiknya berada di kromosom 6p21 dengan ukuran sebesar 3,8 Mb dan berasosiasi dengan lebih dari 100 penyakit berbeda yang  kebanyakan merupakan penyakit autoimun. Proses HLA-typing menggunakan sekuensing Sanger masih memberikan ambiguitas terhadap determinasi alel, low-throughput, dan membutuhkan biaya besar untuk sampel dalam jumlah besar. Next generation sequencing (NGS) menjadi metode yang dapat mengatasi kelemahan sekuensing Sanger. MiSeq dari Illumina merupakan salah satu NGS yang digunakan untuk HLA-typing. MiSeq memberikan kemudahan preparasi dan fleksibilitas metode yang dapat dikembangkan sesuai dengan kebutuhan laboratorium penelitian. Penelitian dilakukan di Laboratorium Molekular Genetik, Laboratorium Terpadu Universitas YARSI pada empat orang mahasiswa Fakultas Kedokteran Universitas YARSI etnik Melayu selama periode Mei–Desember 2014. Hasil menunjukkan terdapat total 546 SNP heterozygous, 888 SNP homozygous, 25 insersi, dan 23 delesi dari keseluruhan 11 sampel amplikon dengan coverage 2.106,536x dengan 2x25 siklus pembacaan. Optimasi metode HLA-typing dapat dikatakan berhasil dengan mengombinasikan long-range PCR dan pemilihan ukuran library 300–600 bp. [MKB. 2015;47(3):152–159]Kata kunci: HLA Kelas I, MiSeq, next generation sequencingDevelopment of Class I HLA Gene In-House HLA-Typing Methods (HLA A, HLA B, and HLA C) using Next Generation Sequencing Illumina MiSeqAbstractHuman leukocyte antigen (HLA) is a 3.8 Mb protein presenting antigen whose genetic locus is located in chromosome 6p21 area and have association with more than 100 different diseases that are mostly autoimmune diseases. HLA-typing process using Sanger sequencing still  creates ambiguity in the  determination of  alleles, low-throughput, and costly as it requires a large quantity of sample. Next generation sequencing (NGS) is a method that can overcome the drawbacks of Sanger sequencing. MiSeq Illumina is one of the NGSs that are used for HLA-typing. This study was conducted at the Laboratory of Molecular, Universitas YARSI in a period from May to December 2014. MiSeq provides convenience and flexibility in the preparation methods that can be developed according to the needs of the research laboratory. The results showed that there were a total of 546 SNPs that were heterozygous, 888homozygous SNP, 25 insertions and 23 deletions from the overall 11 amplicon samples with an average coverage with 2x25 read length of  2,106,536x. Our protocol generates good result as we combined long PCR amplicon and size selection method to 300–600 bp fragment.  [MKB. 2015;47(3):152–159]Key words: HLA Class I, MiSeq, next generation sequencing DOI: 10.15395/mkb.v47n3.389