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"ABSTRAKPemeriksaan mutasi gen PIK3CA penting dilakukan karena mutasi pada gen tersebut menyebabkan penderita kanker payudara dengan subtipe HER 2 mengalami resistensi terhadap terapi trastuzumab. Kit komersial pendeteksi mutasi gen PIK3CA yang beredar di pasaran dibuat berdasarkan genotipe kaukasia/Amerika. Penelitian telah dilakukan untuk mengetahui profil mutasi gen PIK3CA ekson 20 dari penderita kanker payudara di Sumatera Barat. Hasil sekuensing menunjukkan mutasi gen PIK3CA ditemukan 5 dari 68 sampel uji (7,35%) dan paling sering terjadi pada subtipe luminal. Mutasi tersebut berupa silent mutation T1025T (4,41%) dan missense mutation H1047R (2,94%). Hasil penelitian menunjukkan bahwa mutasi gen PIK3CA Ekson 20 tidak berasosiasi dengan keberadaan reseptor ER, PR, dan HER 2. Mutasi yang ditemukan dalam penelitian ini dapat digunakan sebagai referensi pembuatan kit deteksi mutasi gen PIK3CA meskipun tidak berasosiasi dengan parameter patologiklinik.

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ABSTRACTExamination of PIK3CA mutations in breast cancer patients is important because contributed to trastuzumab resistance problem in breast cancer subtype HER 2. Since commercial kit to detect PIK3CA mutation which now widely used were made based on caucasia/America genotype, not based on genotype Indonesia. The research has been conducted to determine the profile of the PIK3CA exon 20 mutations of the breast cancer patients in West Sumatra. Sequencing result showed that 5 out of 68 samples PIK3CA (7.35 %) had PIK3CA mutations and mostly occur in the luminal subtype. Mutations found were silent mutation T1025T (4.41 %) and missense mutation H1047R (2.94%). Meanwhile, this research results that PIK3CA mutation in exon 20 does not associated with the presence of ER, PR, and HER 2 reseptors respectively. However, mutations found in this research was expected to use as a reference in devloping detection kit of PIK3CA mutation regardless the negative association with clinical pathology parameters;"

"Telah dilakukan penelitian untuk deteksi gen PIK3CA ekson 9 dengan pendekatan dua metode PCR dan membandingkan dua metode tersebut, agar menghindari deteksi positif palsu akibat keberadaan pseudogene pada kanker payudara. Sepuluh DNA genomik digunakan pada penelitian ini. Dua pasang primer digunakan untuk metode PCR standar dan Nested PCR untuk deteksi gen PIK3CA ekson 9 dengan ukuran produk PCR adalah 200 bp dan 400 bp diikuti dengan metode DNA sequencing. Optimasi dilakukan untuk menentukan suhu annealing PCR standard dan Nested PCR, serta jumlah siklus yang digunakan pada 1st nested PCR 15 siklus dan 25 siklus. Hasil penelitian menunjukkan PCR standar set primer I dan II bekerja dengan suhu annealing optimum 60,7oC, diinterferensi oleh pseudogene dengan tingkat spesifisitas untuk masing-masingnya sebesar 20 dan 30. Nested PCR dengan kondisi optimum suhu annealing untuk pertama 55oC, suhu annealing kedua 60,7oC dengan 15x siklus PCR berhasil 100 dapat mendeteksi gen PIK3CA. Sampel mengandung satu mutasi substitutsi pada basa 545 ekson 9, mengindikasikan perubahan asam amino dari asam glutamat E ke lisin K. Hasil penelitian menunjukkan bahwa pseudogene terdapat pada kanker payudara. Metode Nested PCR spesifik digunakan untuk studi genotyping gen PIK3CA ekson 9.

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The aim of study is to detect of exon 9 PIK3CA gene with two PCR methods approach and comparing two methods, to avoid detection of false positives effect pseudogene exist in breast cancer. Ten genomics DNA were used in this experiment. Two pairs of primer Standard PCR and Nested PCR method used to detection of exon 9 PIK3CA genes with the size of PCR products is 200 bp and 400 bp followed with DNA sequencing method. Optimization was done to determine of annealing temperature of Standard PCR and Nested PCR, as well as the number of cycles used in the 1st nested PCR 15 cycles and 25 cycles.

The result of research was standard PCR using each primer pairs I and II with optimum annealing temperature 60,7oC, had interference by pseudogene with the degree of specificity for each them was 20 and 30. Nested PCR with optimum condition annealing temperature for the first round at 55oC, annealing temperature for the second round at 60,7oC with 15x PCR cycles 100 succeed to detect the true PIK3CA gene. Samples contain one substitution mutation at position 545 of exon 9, indicating amino acid changing from glutamate acid E to lysin K. The result was, pseudogene also exists in breast cancer. Nested PCR methods specifically used for genotyping studies exon 9 of PIK3CA gene. "

"Latar Belakang : Keganasan kolorektal (KKR) adalah suatu penyakit yang dinamis dan heterogen sehingga untuk mengetahui perangai biologinya membutuhkan identifikasi mutasi gen. KKR melibatkan banyak variasi mutasi gen dan profilnya berbeda-beda antarindividu sehingga penting diketahui pada populasi spesifik. Indonesia hingga kini belum memiliki profil mutasi gen penderita keganasan kolorektal. Penelitian ini bertujuan untuk mendeskripsikan profil mutasi gen yang paling sering terlibat yaitu APC, TP53, PIK3CA, KRAS, dan MLH1 pada penderita KKR di 3 rumah sakit Jakarta. Metode : Penelitian ini adalah penelitian deskriptif yang dilakukan pada penderita KKR yang diberikan terapi bedah dan/atau neoadjuvan dan/atau adjuvan di RSCM, RSKJ, dan MRCCC tahun 2017-2018. Analisis DNA dilakukan dengan menggunakan next-generation sequencing dan disesuaikan dengan GRCh38. Varian patogenik diidentifikasi berdasarkan klasifikasi ACMG dan skor FATHMM. Data klinis dikumpulkan dari rekam medik. Hasil : Terdapat 22 total subjek dengan mutasi patogenik gen APC, TP53, dan PIK3CA yang terjadi 100%, KRAS 64%, dan MLH1 45%. Terjadi 5 jenis mutasi pada kelima gen tersebut yaitu nonsense, missense, frameshift, splice-site, dan silent. Terdapat 4 kelompok co-occurring mutation yang memiliki presentasi klinis berbeda, yaitu APC, TP53, dan PIK3CA (Triple Mutation/TM), TM+KRAS, TM+MLH1, TM+KRAS+MLH1. Kesimpulan : Populasi Indonesia, yang terdiri dari berbagai etnik dengan beragam pola makan dan gaya hidup, memiliki profil mutasi patogenik yang unik dibandingkan negara lain dengan presentasi klinis yang didominasi oleh stadium lokal lanjut dengan luaran dan sintasan yang bervariasi.

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Background : Knowing colorectal cancer’s heterogeneity and dynamic features, recognizing its biological behaviour requires detailed identification of mutated genes involved. Colorectal cancer (CRC) requires several mutated genes to occur and those are dissimilar in each person hence essential to be discovered in specific population. Until recently, there is now known study describing genomic landscape of CRC in Indonesian population. This study aims to describe profile of pathogenic mutation of APC, TP53, PIK3CA, KRAS, and MLH1 in CRC patients treated at 3 different hospitals in Jakarta. Methods : This is a descriptive study conducted on CRC patients who underwent neoadjuvant, surgical, and adjuvant therapy at RSCM, RSKJ, and MRCCC in 2017-2018. DNA analysis was performed using next-generation sequencing and aligned against GRCh38. Pathogenic variant was identified using ACMG classification and FATHMM score. Data related to behaviour and survival were collected from medical records Results : There were total 22 subjects in which APC, TP53, and PIKCA were mutated. KRAS mutation occurred in 64%, while MLH1 in 45%. Five types of mutation were identified, including nonsense, missense, frameshift, splice-site, and silent mutation. There are 4 groups of co-occurring mutations, which are APC, TP53, PIK3CA (triple mutation/TM) alone; TM+KRAS; TM+MLH1; and TM+KRAS+MLH1, presenting different nature and survival. Conclusion : Indonesia having various ethnicities with diverse diet and lifestyle has distinct profile of pathogenic mutation presenting mostly with locally-advanced stage with various outcome and survival rate."