Archival bone marrow samples: suitable for multiple biomarker analysis?

Bendik Lund; Laeya A Najmi; Agata Wesolowska-Andersen; Veslemøy M Landsem; Kirsten K Rasmussen; Louise Borst; Ramneek Gupta; K. Schmiegelow; Helge Klungland

doi:10.1097/PDM.0000000000000032

Archival bone marrow samples: suitable for multiple biomarker analysis?

Bendik Lund, Laeya A Najmi, Agata Wesolowska-Andersen, Veslemøy M Landsem, Kirsten K Rasmussen, Louise Borst, Ramneek Gupta, K. Schmiegelow, Helge Klungland

Department of Clinical Medicine

1 Citation (Scopus)

Abstract

Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

Original language	English
Journal	Applied Immunohistochemistry & Molecular Morphology
Volume	23
Issue number	1
Pages (from-to)	71-7
Number of pages	7
ISSN	1541-2016
DOIs	https://doi.org/10.1097/PDM.0000000000000032
Publication status	Published - 14 Jan 2015

Keywords

Adolescent
Biomarkers, Tumor
Biopsy
Bone Banks
Bone Marrow
Child
Child, Preschool
DNA
Denmark
Female
Fluorometry
Genome
Genotype
Humans
Male
Microsatellite Repeats
Norway
Pilot Projects
Polymorphism, Single Nucleotide
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Specimen Handling
Spectrophotometry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1097/PDM.0000000000000032

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title = "Archival bone marrow samples: suitable for multiple biomarker analysis?",

abstract = "Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.",

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author = "Bendik Lund and Najmi, {Laeya A} and Agata Wesolowska-Andersen and Landsem, {Veslem{\o}y M} and Rasmussen, {Kirsten K} and Louise Borst and Ramneek Gupta and K. Schmiegelow and Helge Klungland",

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doi = "10.1097/PDM.0000000000000032",

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T1 - Archival bone marrow samples

T2 - suitable for multiple biomarker analysis?

AU - Lund, Bendik

AU - Najmi, Laeya A

AU - Wesolowska-Andersen, Agata

AU - Landsem, Veslemøy M

AU - Rasmussen, Kirsten K

AU - Borst, Louise

AU - Gupta, Ramneek

AU - Schmiegelow, K.

AU - Klungland, Helge

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N2 - Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

AB - Archival samples represent a significant potential for genetic studies, particularly in severe diseases with risk of lethal outcome, such as in cancer. In this pilot study, we aimed to evaluate the usability of archival bone marrow smears and biopsies for DNA extraction and purification, whole genome amplification (WGA), multiple marker analysis including 10 short tandem repeats, and finally a comprehensive genotyping of 33,683 single nucleotide polymorphisms (SNPs) with multiplexed targeted next-generation sequencing. A total of 73 samples from 21 bone marrow smears and 13 bone marrow biopsies from 18 Danish and Norwegian childhood acute lymphoblastic leukemia patients were included and compared with corresponding blood samples. Samples were grouped according to the age of sample and whether WGA was performed or not. We found that measurements of DNA concentration after DNA extraction was dependent on detection method and that spectrophotometry overestimated DNA amount compared with fluorometry. In the short tandem repeat analysis, detection rate dropped slightly with longer fragments. After WGA, this drop was more pronounced. Samples stored for 0 to 3 years showed better results compared with samples stored for 4 to 10 years. Acceptable call rates for SNPs were detected for 7 of 42 archival samples. In conclusion, archival bone marrow samples are suitable for DNA extraction and multiple marker analysis, but WGA was less successful, especially when longer fragments were analyzed. Multiple SNP analysis seems feasible, but the method has to be further optimized.

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KW - Child, Preschool

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KW - Denmark

KW - Female

KW - Fluorometry

KW - Genome

KW - Genotype

KW - Humans

KW - Male

KW - Microsatellite Repeats

KW - Norway

KW - Pilot Projects

KW - Polymorphism, Single Nucleotide

KW - Precursor Cell Lymphoblastic Leukemia-Lymphoma

KW - Specimen Handling

KW - Spectrophotometry

U2 - 10.1097/PDM.0000000000000032

DO - 10.1097/PDM.0000000000000032

M3 - Journal article

C2 - 25621358

SN - 1541-2016

VL - 23

SP - 71

EP - 77

JO - Applied Immunohistochemistry & Molecular Morphology

JF - Applied Immunohistochemistry & Molecular Morphology

IS - 1

ER -

Archival bone marrow samples: suitable for multiple biomarker analysis?

Abstract

Keywords

UN SDGs

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