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Kubar A, Temel SG, Beken S, Onder G, Hatirnaz O, Korkmaz A, Alanay Y, Ozbek U, Sag SO, Ergoren MC, Kubar E, Sonmezalp CZ, Doğan O. A new line method; A direct test in spinal muscular atrophy screening for DBS. Mol Genet Genomic Med 2023; 11:e2270. [PMID: 37614112 PMCID: PMC10724511 DOI: 10.1002/mgg3.2270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Nucleic acid-based assays provide an opportunity to screen for genetically encoded diseases like spinal muscular atrophy (SMA), before the onset of symptoms. Nowadays, such assays could be easily utilized as high-throughputs in SMA to detect a homozygous deletion of exon 7 of the survival motor neuron 1 gene (SMN1) that is responsible for >95% of SMA patients. METHODS We developed a new line method (NLM) as a direct real time PCR test procedure without nucleic acid extraction in dried blood spots (DBS) to screen for homozygous deletion of exon 7 of the SMN1 gene. Performance of this setup was evaluated on 580 DBS newborn samples and air dried 50 DBS from whole blood including 20 samples for homozygous deletion of the SMN1 gene detected earlier with MLPA. RESULTS We found all 580 newborn DBS samples as wild type. DBS prepared from 50 whole blood samples also including 20 affected people were correctly identified as homozygous deletions and 30 wild types of exon 7 of SMN1 as before with MLPA. When the MLPA method was taken as the gold standard, the sensitivity and specificity of the NLM test were found 100% for the detection of SMN1 exon 7 homozygous deletion. CONCLUSION In the NLM, the total test duration has been reduced to less than 75 min without requiring any extra process such as DNA extraction step and sample plate preparation after the punching step. Thereby, newborn SMA screening with the NLM has gained an environmentally friendly feature with not requiring additional tedious steps.
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Affiliation(s)
| | - Sehime Gülsüm Temel
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
- Department of Translational Medicine, Institute of Health SciencesBursa Uludag UniversityBursaTurkey
| | - Serdar Beken
- Department of Pediatrics, School of MedicineAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Gizem Onder
- Department of Biochemistry and Molecular Biology, Institute of of Health SciencesAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Ozden Hatirnaz
- Department of Basic Sciences, Medical Biology, School of MedicineAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Ayse Korkmaz
- Department of Pediatrics, School of MedicineAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Yasemin Alanay
- Department of Pediatrics, School of MedicineAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Ugur Ozbek
- Department of Medical Sciences, Medical Genetics, School of MedicineAcibadem Mehmet Ali Aydınlar UniversityIstanbulTurkey
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | | | - Elif Kubar
- Ege University Faculty of MedicineDepartment of Medical GeneticsIzmirTurkey
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Bouike Y, Sakima M, Taninishi Y, Matsutani T, Noguchi Y, Bo R, Awano H, Nishio H. Real-Time PCR-Based Screening for Homozygous SMN2 Deletion Using Residual Dried Blood Spots. Genes (Basel) 2023; 14:2159. [PMID: 38136980 PMCID: PMC10742981 DOI: 10.3390/genes14122159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The survival motor neuron 2 (SMN2) gene is a recognized modifier gene of spinal muscular atrophy (SMA). However, our knowledge about the role of SMN2-other than its modification of SMA phenotypes-is very limited. Discussions regarding the relationship between homozygous SMN2 deletion and motor neuron diseases, including amyotrophic lateral sclerosis, have been mainly based on retrospective epidemiological studies of the diseases, and the precise relationship remains inconclusive. In the present study, we first estimated that the frequency of homozygous SMN2 deletion was ~1 in 20 in Japan. We then established a real-time polymerase chain reaction (PCR)-based screening method using residual dried blood spots to identify infants with homozygous SMN2 deletion. This method can be applied to a future prospective cohort study to clarify the relationship between homozygous SMN2 deletion and motor neuron diseases. In our real-time PCR experiment, both PCR (low annealing temperatures) and blood (high hematocrit values and low white blood cell counts) conditions were associated with incorrect results (i.e., false negatives and positives). Together, our findings not only help to elucidate the role of SMN2, but also aid in our understanding of the pitfalls of current SMA newborn screening programs for detecting homozygous SMN1 deletions.
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Affiliation(s)
- Yoshihiro Bouike
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Makoto Sakima
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Yuya Taninishi
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan; (Y.B.); (M.S.); (Y.T.)
| | - Takanori Matsutani
- Division of Physiology, Shinko Hospital, 1-4-47 Wakinohama-cho, Chuo-ku, Kobe 651-0072, Japan;
| | - Yoriko Noguchi
- Department of Clinical Laboratory, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Ryosuke Bo
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan;
| | - Hiroyuki Awano
- Organization for Research Initiative and Promotion, Research Initiative Center, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan;
| | - Hisahide Nishio
- Department of Occupational Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan
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Wijaya YOS, Nishio H, Niba ETE, Okamoto K, Shintaku H, Takeshima Y, Saito T, Shinohara M, Awano H. Detection of Spinal Muscular Atrophy Patients Using Dried Saliva Spots. Genes (Basel) 2021; 12:genes12101621. [PMID: 34681015 PMCID: PMC8535962 DOI: 10.3390/genes12101621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a lower motor neuron disease, once considered incurable. The main symptoms are muscle weakness and muscular atrophy. More than 90% of cases of SMA are caused by homozygous deletion of survival motor neuron 1 (SMN1). Emerging treatments, such as splicing modulation of SMN2 and SMN gene replacement therapy, have improved the prognoses and motor functions of patients. However, confirmed diagnosis by SMN1 testing is often delayed, suggesting the presence of diagnosis-delayed or undiagnosed cases. To enable patients to access the right treatments, a screening system for SMA is essential. Even so, the current newborn screening system using dried blood spots is still invasive and cumbersome. Here, we developed a completely non-invasive screening system using dried saliva spots (DSS) as an alternative DNA source to detect SMN1 deletion. In this study, 60 DSS (40 SMA patients and 20 controls) were tested. The combination of modified competitive oligonucleotide priming-polymerase chain reaction and melting peak analysis clearly distinguished DSS samples with and without SMN1. In conclusion, these results suggest that our system with DSS is applicable to SMA patient detection in the real world.
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Affiliation(s)
- Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
- Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Hyogo, Japan
- Correspondence: ; Tel.: +81-789-745-073
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, 4-5-5 Ishiicho, Imabari 794-0006, Ehime, Japan;
| | - Haruo Shintaku
- Department of Pediatrics, Osaka City University Graduate School of Medicine, 1-4-3 Asahi-Machi, Abeno-ku, Osaka 545-8585, Osaka, Japan;
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, 1-1 Mukogawacho, Nishinomiya 663-8501, Hyogo, Japan;
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, 5-1-1 Toneyama, Toyonaka 560-8552, Osaka, Japan;
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Hyogo, Japan;
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