Relapse samples from a total of 123 BCP-ALL patients were included in this study, all of which were obtained from the DCOG biobank with informed consent. These patients were treated according to one of 3 DCOG treatment studies ALL8 (n = 39), ALL9 (n = 55) or ALL10 (n = 29). The patients included were a good representation of the total cohort of relapsed patients from these trials with respect to gender, risk group, remission time, and ploidy status at diagnosis, with the exception of remission time in ALL8 relapses (Table S2, Supplemental Digital Content). No infant ALL patients were included in this cohort. Patient characteristics are listed in Table S3 (Supplemental Digital Content). To investigate whether relapse-associated genetic alterations were also present at diagnosis, 77 available paired diagnosis samples were analyzed. Mononuclear cells were isolated by Ficoll gradient separation and stored in liquid nitrogen. Genomic DNA was extracted from mononuclear cells and purified using a QIAamp purification kit (Qiagen, Venlo, The Netherlands).
Qiaamp purification kit
Manufactured by Qiagen
Sourced in Germany
The QIAamp purification kit is a laboratory equipment product designed for the purification of nucleic acids, including DNA and RNA, from various sample types. The kit utilizes silica-based spin columns to efficiently bind, wash, and elute the target molecules. It provides a simple and reliable method for extracting high-quality nucleic acids for further analysis or downstream applications.
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Lab products found in correlation
Expand high fidelity enzyme mix, by Roche (1 mentions)
T4 gene 32 protein, by Roche (1 mentions)
Bovine serum albumin (bsa), by New England Biolabs (1 mentions)
Dntp mix, by Thermo Fisher Scientific (1 mentions)
Expand high fidelity buffer, by Roche (1 mentions)
Bigdye terminator kit version 3, by Thermo Fisher Scientific (1 mentions)
Qiaamp viral rna extraction kit, by Qiagen (1 mentions)
3130 genetic analyzer, by Thermo Fisher Scientific (1 mentions)
Surecycler 8800 thermal cycler, by Agilent Technologies (1 mentions)
4 protocols using qiaamp purification kit
1
Relapse Genetics in Pediatric BCP-ALL
2
Amplification and Purification of 16S rDNA
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Hypervariable rrs gene V5-V6 regions of about 280 bp were amplified with 784F 5′-AGGATTAGATACCCTGGTA-3′ and 1061R 5′-CRRCACGAGCTGACGAC-3′ primers (Andersson et al., 2008 (link)). These primers were selected in silico with the RDP Probe Match tool according to the following criteria (Cole et al., 2009 (link)): hybridization with 94% of sequences belonging to the RDP Bacteria domain database with good quality and ≥1200 bp long with 2 mismatches allowed in primer sequences. In addition, Basic Local Alignment Search Tool (BLAST) was used to check that the chosen primers did not match Ae. albopictus 18S and mitochondrial 16S rDNA gene sequences. PCR amplification was performed using 1.75 U of Expand High Fidelity Enzyme Mix (Roche, Switzerland) with 1× Expand High Fidelity Buffer (Roche, Switzerland), 0.06 mg mL−1 of T4 gene 32 protein (Roche, France), 0.06 mg mL−1 of bovine serum albumin (New England Biolabs, France), 40 μM of dNTP mix, 200 nM of each primer (Invitrogen, France) and 30 ng of template DNA. PCR products were purified with QiaAmp purification kit (Qiagen, France) following the manufacturer's recommendations.
3
Genetic Surveillance of H5N1 Influenza in Egypt
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The H5N1 HPAI virus isolates and field samples from 368 cases of H5N1 were collected in Egypt during the period from 2006 to 2014. They were collected from different localities in Lower and Upper Egypt, different bird species (chicken, duck, turkey, geese, quail and ostrich) and different poultry value chain nodes like households, commercial poultry farms and live bird markets.
The full length HA gene sequencing has been conducted, where the ribonucleic acids (RNAs) of virus isolates or samples were extracted using QiaAmp viral RNA extraction kit (Qiagen, Germany) according to the manufacturer’s instructions. A one-step RT-PCR was conducted on the extracted RNAs using specific primers for Matrix (M) and H5 genes [29 (link), 30 (link)]. The PCR products were purified using a QiaAmp purification kit (Qiagen, Germany). The HA gene sequencing was done using a Bigdye Terminator Kit (version 3.1; Applied Biosystems, Foster City, CA) on a 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). The sequencing of the HA gene was conducted at NLQP and the data were regularly submitted to the GenBank and are available at the National Center for Biotechnology Information (NCBI) Influenza Virus Resource. Recently, new sequence data from 2012–2014 were added in the GenBank under accession numbers of KJ522707-KJ522745 and KP209286-KP209303.
The full length HA gene sequencing has been conducted, where the ribonucleic acids (RNAs) of virus isolates or samples were extracted using QiaAmp viral RNA extraction kit (Qiagen, Germany) according to the manufacturer’s instructions. A one-step RT-PCR was conducted on the extracted RNAs using specific primers for Matrix (M) and H5 genes [29 (link), 30 (link)]. The PCR products were purified using a QiaAmp purification kit (Qiagen, Germany). The HA gene sequencing was done using a Bigdye Terminator Kit (version 3.1; Applied Biosystems, Foster City, CA) on a 3130 Genetic Analyzer (Applied Biosystems, Foster City, CA). The sequencing of the HA gene was conducted at NLQP and the data were regularly submitted to the GenBank and are available at the National Center for Biotechnology Information (NCBI) Influenza Virus Resource. Recently, new sequence data from 2012–2014 were added in the GenBank under accession numbers of KJ522707-KJ522745 and KP209286-KP209303.
4
TFAM Exon 4 Amplification Protocol
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The amplification of exon 4 of TFAM was performed as stated previously.2 (link) The PCR was conducted using the SureCycler 8800 Thermal Cycler (Agilent Technologies, Inc., Santa Clara, Calif, USA). A volume of 20 µL total reaction was performed using Phusion High Fidelity (ThermoFisher Scientific) for 30 cycles of 98°C for 10 seconds, 68°C for 30 seconds, and 72°C for 30 seconds, and a final elongation at 72°C for 7 minutes. The PCR products were then purified using QIAamp Purification Kit (QIAGEN, Hilden, Germany).
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