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Quickgene 610l

Manufactured by Fujifilm
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Sourced in Japan, France

The QuickGene-610L is a fully automated nucleic acid extraction system developed by Fujifilm. It is designed to efficiently extract DNA, RNA, and other nucleic acids from a variety of sample types. The system features a compact and user-friendly design, making it suitable for use in clinical, research, and diagnostic laboratories.

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QuickGene-610L system (4 citations) QuickGene-610L equipment (3 citations) QuickGene-610L DNA extraction kit (2 citations) QuickGene-610L Nucleic Acid Isolation System (2 citations)

30 protocols using quickgene 610l

1

Whole-Exome Sequencing for Genetic Variant Identification

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Genomic DNA was obtained from peripheral blood leukocytes of all individuals using QuickGene 610L (Wako, Osaka, Japan). We performed whole-exome sequencing (WES) as previously described12 (link). In brief, genomic DNA was captured using SureSelect Human All Exon V5 or V6 (Agilent Technologies, Santa Clara, CA, USA), and the captured libraries were sequenced on an Illumina HiSeq 2500 with 101-bp paired-end reads. Image analysis and base calling were performed using sequence control software with real-time analysis and CASAVA software (Illumina, San Diego, CA, USA). Sequence reads were aligned to GRCh37 using Novoalign (http://www.novocraft.com/). Local realignments around indels and base quality score recalibration were performed using Picard (http://picard.sourceforge.net/) and the Genome Analysis Toolkit (GATK; https://www.broadinstitute.org/gatk/index.php). Variants were called by GATK UnifiedGenotyper and filtered according to GATK Best Practices V3 (https://software.broadinstitute.org/gatk/). Included variants were annotated using ANNOVAR software (http://annovar.openbioinformatics.org/) after excluding common variants registered in the common dbSNP135 data (minor allele frequency > 0.01). The detected variants were confirmed by Sanger sequencing.
Itai T., Sugie A., Nitta Y., Maki R., Suzuki T., Shinkai Y., Watanabe Y., Nakano Y., Ichikawa K., Okamoto N., Utsuno Y., Koshimizu E., Fujita A., Hamanaka K., Uchiyama Y., Tsuchida N., Miyake N., Misawa K., Mizuguchi T., Miyatake S, & Matsumoto N. (2023). A novel NONO variant that causes developmental delay and cardiac phenotypes. Scientific Reports, 13, 975.
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2

Genotyping AGXT2 SNPs from Blood

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After 7 mL of blood samples treated with EDTA were stored at 2–5 °C within 3 days, blood samples were centrifuged at room temperature and the buffy coat was collected. Genomic DNA was prepared from the buffy coat using a DNA extraction kit (QuickGene-610L; FUJIFILM Wako Pure Chemical Corp., Osaka, Japan) and stored at − 20 °C. According to the manufacturer’s instructions, four AGXT2 SNPs, rs37370 (C__1018750_1_), rs37369 (C__11162986_1_), rs180749 (C__1018735_1_), and rs16899974 (C__25742181_10), were genotyped using the prestandardized and experimentally validated TaqMan SNP genotyping assay on the StepOnePlus machine (Applied Biosystems, Foster City, CA, USA).
Kumon H., Miyake Y., Yoshino Y., Iga J.I., Tanaka K., Senba H., Kimura E., Higaki T., Matsuura B., Kawamoto R, & Ueno S.I. (2024). Functional AGXT2 SNP rs180749 variant and depressive symptoms: Baseline data from the Aidai Cohort Study in Japan. Journal of Neural Transmission, 131(3), 267-274.
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3

Exome Sequencing and Variant Analysis

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Genomic DNA was isolated from peripheral blood leukocytes using QuickGene 610L (Wako). It was then captured using the SureSelect Human All Exon v5 (50 Mb) or v6 (60 Mb) Kit (Agilent Technologies) and sequenced on an Illumina HiSeq2500 (Illumina) with 101-bp paired-end reads. Exome data processing, variant calling, and variant annotation were performed as previously described (Seyama et al., 2023 (link)). The average read depth of protein-coding regions was >60× and at least 90% of target bases were sequenced by 10 or more reads. Common single-nucleotide polymorphisms with minor allele frequencies ≥1% in dbSNP 137 and variants observed in more than 5 of 575 in-house ethnically matched control exomes were filtered out. Among the remaining rare variants, focus was placed on amino acid-altering or splicing-affecting variants. Candidate variants were confirmed by Sanger sequencing of PCR products using an ABI PRISM 3500xl genetic analyzer (Life Technologies) using genomic DNA from the patient and parents as a template.
Takeda Y., Ueki M., Matsuhiro J., Walinda E., Tanaka T., Yamada M., Fujita H., Takezaki S., Kobayashi I., Tamaki S., Nagata S., Miyake N., Matsumoto N., Osawa M., Yasumi T., Heike T., Ohtake F., Saito M.K., Toguchida J., Takita J., Ariga T, & Iwai K. (2024). A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome. The Journal of Experimental Medicine, 221(6), e20231941.
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4

Genotyping AGXT2 SNPs in Peripheral Blood

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Genomic DNA was prepared from peripheral blood using a DNA extraction kit (QuickGene-610L; Fujifilm Wako Pure Chemical Corp, Osaka, Japan). Four AGXT2 SNPs, rs37370 (C_1018750_1_), rs37369 (C_11162986_1_), rs180749 (C_1018735_1_) and rs16899974 (C_25742181_10), were genotyped using the pre-standardized and experimentally validated TaqMan SNP genotyping assay on a StepOnePlus machine (Applied Biosystems, Foster City, California, United States), according to the manufacturer's instructions.
Kumon H., Miyake Y., Yoshino Y., Iga J.I., Tanaka K., Senba H., Kimura E., Higaki T., Matsuura B., Kawamoto R, & Ueno S.I. (2022). Functional AGXT2 SNP rs37369 Variant Is a Risk Factor for Diabetes Mellitus: Baseline Data From the Aidai Cohort Study in Japan. Canadian journal of diabetes, 46(8).
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5

Exome Sequencing of KIF1A Variants

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Genomic DNA was obtained from peripheral blood leukocytes using Quick-Gene 610L (Wako, Osaka, Japan). Genomic DNA was captured using the SureSelect Human All Exon v4 or v5 Kit (51 Mb; Agilent Technologies, Santa Clara, CA, USA) and sequenced on a HiSeq2000 (Illumina, San Diego, CA, USA) with 101-bp paired-end reads. Exome data processing, variant calling and variant annotation were performed as described previously. 10 Rare nonsynonymous KIF1A variants, which were absent in 137, the 6500 exomes of the National Heart, Lung and Blood Institute exome project, and our in-house 575 control exomes, were considered as candidate KIF1A mutations, and their segregation was examined by Sanger sequencing with trio samples (patients and their parents). In families showing de novo mutations, parentage was confirmed by microsatellite analysis, as previously described. 11 Pathogenicity of the mutations was predicted using Sorting Intolerant from Tolerant (SIFT; http://sift.jcvi.org/), Polyphen2 (http://genetics.bwh.harvard.edu/pph2/) and Mutation Taster (http://www.mutationtaster.org/). KIF1A mutations were annotated based on transcript variant 1 (NM_001244008.1). The de novo KIF1A mutations were deposited to a gene-specific database (http://databases.lovd.nl/ shared/genes/KIF1A).
Ohba C., Haginoya K., Osaka H., Kubota K., Ishiyama A., Hiraide T., Komaki H., Sasaki M., Miyatake S., Nakashima M., Tsurusaki Y., Miyake N., Tanaka F., Saitsu H, & Matsumoto N. (2015). De novo KIF1A mutations cause intellectual deficit, cerebellar atrophy, lower limb spasticity and visual disturbance. Journal of human genetics, 60(12).
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6

Genetic Analysis of Developmental Encephalopathies

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A total of 700 individuals with developmental and epileptic encephalopathies were analyzed. Among them, 210 individuals were analyzed with their parents. Clinical information was obtained and peripheral blood leukocytes were collected from the patients and their parents after obtaining their written informed consent. DNA was extracted using QuickGene‐610L (Fujifilm, Tokyo, Japan) according to the manufacturer's instructions. The study was approved by the institutional review boards of the Yokohama City University School of Medicine and the Showa University School of Medicine.
Shiraku H., Nakashima M., Takeshita S., Khoo C., Haniffa M., Ch'ng G., Takada K., Nakajima K., Ohta M., Okanishi T., Kanai S., Fujimoto A., Saitsu H., Matsumoto N, & Kato M. (2018). PLPBP mutations cause variable phenotypes of developmental and epileptic encephalopathy. Epilepsia Open, 3(4), 495-502.
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7

Genomic DNA Extraction and SNP Genotyping

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Genomic DNA from all participants was isolated from whole blood samples using Quick Gene-610L assays (Fujifilm, Tokyo, Japan). The DNA concentration was adjusted to 10–15 ng/μL for SNP genotyping experiments. Two eQTL SNPs at rs9264942 and rs2395471 were selected based on a previous study22 (link),23 (link). Three SNPs at rs2270191, rs3132550, and rs6915986, which were in strong LD with the HLA-C*12:02~B*52:01~DRB1*15:02 haplotype, were also adopted based on an earlier report22 (link). The genotyping of five SNPs located at rs9264942, rs2395471, rs2270191, rs3132550, and rs6915986 was performed with a TaqMan 5 exonuclease assay using primers supplied by Applied Biosystems (Foster City, CA, USA). The probe’s fluorescence signal was detected with a StepOne Plus Real-Time PCR System (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Suzuki H., Joshita S., Hirayama A., Shinji A., Mukawa K., Sako M., Yoshimura N., Suga T., Umemura T., Ashihara N., Yamazaki T, & Ota M. (2020). Polymorphism at rs9264942 is associated with HLA-C expression and inflammatory bowel disease in the Japanese. Scientific Reports, 10, 12424.
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8

Genetic Markers for Age-Related Macular Degeneration

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Genotyping data were available for 18 and 35 patients in the combination and IVR groups, respectively. Genomic DNA was extracted from peripheral blood samples using a DNA extraction kit (QuickGene-610 L; Fujifilm, Minato, Tokyo, Japan). Genes encoding age-related maculopathy susceptibility protein 2 (ARMS2) A69S rs10490924 and complement factor H I62V rs800292 were genotyped by the TaqMan single-nucleotide polymorphism assay method using the ABI PRISM 7700 system (Applied Biosystems, Foster City, CA, USA).
Miyata M., Ooto S., Yamashiro K., Tamura H., Hata M., Ueda-Arakawa N., Yoshikawa M., Numa S, & Tsujikawa A. (2019). Five-year visual outcomes after anti-VEGF therapy with or without photodynamic therapy for polypoidal choroidal vasculopathy. The British journal of ophthalmology, 103(5).
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9

Genotyping of AMD-Associated SNPs

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Genotyping was performed in 92 patients. Genomic DNA was prepared from leukocytes of peripheral blood using a DNA extraction kit (QuickGene-610L; Fujifilm, Tokyo, Japan). We genotyped the major AMD-associated single nucleotide polymorphisms, i.e., ARMS2 A69S rs10490924, CFH I62V rs800292, and CFH Y402H rs1061170, using TaqMan ANP assays with the ABI PRISM 7700 system (Applied Biosystems Inc, Foster City, CA). I
Tagawa M., Ooto S., Yamashiro K., Tamura H., Oishi A., Miyata M., Hata M., Yoshikawa M., Yoshimura N, & Tsujikawa A. (2020). Characteristics of pachychoroid neovasculopathy. Scientific Reports, 10, 16248.
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10

Genotyping IL4RA Regulatory Variants

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Genomic DNA was extracted from peripheral blood samples using an automated DNA extraction system (QuickGene-610L; Fujifilm, Tokyo, Japan). The typing of rs8832, which is an expression quantitative trait locus and splicing quantitative trait locus of IL4RA, was performed using the Infinium Asian Screening Array (Illumina, San Diego, CA, USA) or the Illumina HumanHap 550v3/610-Quad BeadChip (Illumina) [13 (link)].
Hyodo K., Masuko H., Oshima H., Shigemasa R., Kitazawa H., Kanazawa J., Iijima H., Ishikawa H., Kodama T., Nomura A., Kagohashi K., Satoh H., Saito T., Sakamoto T, & Hizawa N. (2022). Common exacerbation-prone phenotypes across asthma and chronic obstructive pulmonary disease (COPD). PLoS ONE, 17(3), e0264397.
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