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Annex I Transcriptions of selected articles

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Annex I Transcriptions of selected articles ...

    thFigure 1: Full search strategy carried out on 11 May 2007

    Aim: To identify all original articles published in English in 2006 investigating the diagnostic

    value of molecular, genetic or proteomic tests.

    MAIN SEARCH

    Genomics [MeSH] OR Microarray analysis [MeSH]

    AND Diagnosis [MeSH]

    not review, not letter, not editorial, not case report

    LIMITS: Year of publication 2006, English language

    1402 abstract identified

    ADDTIONAL SEARCH TO IMPROVE SENSITIVITY

    [2]

    “Sensitivity and Specificity”

    [MeSH]

    AND “Diagnos*” AND

    “genomics” or “proteomics”

    [1] [3] “Molecular Diagnostic “genetic” or “molecular”

    Techniques” [MeSH] AND

     “diagnostic test”

    [4]

    [1] OR [2] OR [3]

    not review, not letter, not

    editorial, not case report

    LIMITS: Year of

    publication 2006,

    English language

    222 abstracts identified

    Annex I: Transcriptions of selected articles

Reference Study Statements regarding use Statements regarding Overinterpretation

    in annex 2 design for clinical diagnosis further validation studies

    (25) Alternative Definitively favourable: Yes Further validation:

    diagnosis „MS-MA appears to be an Additional study with more

    control efficient primary method to samples and different types of

    diagnose PWS/AS. pathogenesis for both PWS

    Therefore, this rapid MS-MA and AS may be necessary to

    is a good primary screening determine the sensitivity and

    method that can be accuracy of both the MS-MA

    implemented in a diagnostic and MS-MLPA assays‟.

    laboratory to determine the

    methylation patterns of

    patients with suspected PWS

    or A‟.

    (41) Healthy Definitively favourable: Further validation: „If Yes

    control „The results suggest that a prospectively validated in a

    peripheral blood larger population, may provide

    mononuclear cell-based gene the basis for a molecular

    expression signature can diagnosis of UC and CD and

    provide a molecular contribute to the diagnosis of

    biomarker that can patients classified as

    complement the standard indeterminate IBD‟.

    diagnosis of UC and CD‟.

    (26) Alternative Definitively favourable: Yes Not mention of further

    diagnosis „These assays may be validation.

    control reliably applied as a

    diagnostic test or large scale

    method for population

    screening‟.

    (48) Alternative Definitively favourable: Yes Not mention of further

    diagnosis „We therefore conclude that validation.

    control elevations of MLCLs are

    specific for BTHS and that

    the MLCL/CL ratio in

    fibroblasts is a better

    diagnostic marker than CL

    alone‟

    (29) Healthy Promising: „These data No Further validation:

    control indicated that these peak „Additional studies are

    could be used as potential required to validate these

    biomarkers for gastric patterns as unique “malignant”

    cancer‟ protein signatures before they

    can be used with confidence to

    identify and screen populations

    at high risk for gastric cancer‟.

Reference Study Statements regarding use Statements regarding Overinterpretation

    in annex 2 design for clinical diagnosis further validation studies

    (40) Healthy Promising: „This study Further validation: „Further No

    control shows that free-circulating studies are needed to

    DNA can be detected in understand the correlation of

    cancer patients compared these new molecular markers

    with disease-free individuals, with cancer diagnosis,

    and suggests a new, non outcome of disease, and

    invasive approach for early eventually treatment response‟

    detection of cancer‟.

    (30) Healthy Promising: ‘The present Yes Not mention of further

    control study of the CSF proteins validation.

    secreted in patients with

    INPH suggests that certain

    CSF proteins may be useful

    adjuncts in the clinical

    diagnosis of INPH‟.

    (35) Alternative Promising: „The ability to Yes Not mention of further

    diagnosis demonstrate MSI in validation.

    control heterogenous endometrial

    samples suggests potential

    for the development of a

    novel EC screening tool for

    women in HNPCC kindreds‟

    (36) Other: Unfavourable: „Screening No Not mention of further

    series of for MMR deficiency should validation.

    cases not be applied routinely in

    adenomas with the goal to

    identify HNPCC patients‟.

    (37) Other: Promising: ‘Real-time PCR Yes Not mention of further

    series of on CSF samples seems a validation.

    cases promising adjunct for

    diagnosis of mumps

    meningitis, especially in an

    age group with high

    incidence of mumps‟-

    (39) Other: Promising: „It suggests that Further validation: „Further No

    series of the assay will work on validation of the assay with

    cases samples that are more likely larger numbers of true and

    to be poorly differentiated resolved CUP samples will be

    and more representative of needed to assess not only the

    the true clinical dilemma‟. true clinical value of such

    molecular techniques but also

    the ability of new information

    to impact survival and quality

    of life‟.

Reference Study Statements regarding use Statements regarding Overinterpretation

    in annex 2 design for clinical diagnosis further validation studies (43) Other: Further validation: „Other Yes Definitively favourable:

    highly „The ability to rapidly plans include further studies

    selected identify new, potentially with larger numbers and

    cohort pandemic strains of influenza varieties of isolates and patient

    supplies virus will allow health care samples‟.

    by CDC to officials to more rapidly

    include all respond and, potentially,

    types. reduce the spread and human

    impact of the disease‟.

    (71) Other Yes Definitively favourable: Not mention of further

    „This study demonstrates that validation.

    microarray is useful for

    simultaneous monitoring of

    several viruses and their

    subtypes‟.

    (50) Clinically Unfavourable: „However, Further validation: „The - No

    relevant many challenges remain success of this approach must

    population before PCR can be be proven on a much larger

    recommended for the scale using multiple sites‟

    diagnosis of sepses.

    (87) Clinically Definitively favourable: Further validation: „The - No (according to

    relevant „Component-based testing clinical relevance of each study design)

    population and the whole-allergen CAP allergen needs to be validated - No (according to

    are equally relevant in the separately prior to the accuracy): Sensitivity:

    diagnosis of grass-, birch- implementation of multi-72%; specificity: 92%.

    and cat-allergic patients‟. allergen panels into routine

    diagnostic settings‟. (105) Clinically Definitively favourable: - No (according to Further validation:

    relevant „Use of array-CGH should „Additional large-scale studies study design)

    population increase the detection of are required in order to - Yes, due to lack of

    abnormalities relative to the determine whether array-CGH accuracy index.

    risk, and is an option for an may eventually replace a

    enhanced level of screening karyotype in routine prenatal

    for chromosomal diagnoses.

    abnormalities in high risk

    pregnancies‟.

    (38) Clinically Definitively favourable: „A - No (according to Not mention of further

    relevant semi-automated and study design) validation.

    population simplified molecular - No (according to

    diagnostic protocol for the accuracy): Sensitivity:

    rapid detection of Norovirus 100%; specificity: 66%.

    has been achieved‟. (42) Clinically Definitively favourable: - No (according to Not mention of further

    relevant „Our results indicated that the study design) validation.

    population developed assay is reliable as - No (according to

    well as time and cost accuracy): Accuracy

    effective for clinical 100%.

    diagnosis of chromosome

    22q11.2 deletion‟.

Reference Study Statements regarding use Statements regarding Overinterpretation

    in annex 2 design for clinical diagnosis further validation studies (54) Clinically Definitively favourable: - No (according to Not mention of further

    relevant „This PCR assay detects a study design) validation.

    population variety of strains exhibiting - Yes, due to lack of

    characteristics of the EAEC accuracy index.

    group, making it a useful tool

    for identifying both typical

    and atypical EAEC‟.

    (91) Clinically Promising: „Using SELDI-No Further validation:

    relevant TOF analysis of 195 unique „Additional studies are going

    population specimens, we discovered on to further identify and

    with preliminary validation validate these biomarkers‟

    six distinct peaks that may

    potentially be useful in the

    detection and monitoring of

    ovarian cancer‟.

    Annex 2: References of 108 articles analysed.

    1- Villanueva J, Martorella AJ, Lawlor K et al. Serum peptidome patterns that

    distinguish metastatic thyroid carcinoma from cancer-free controls. Mol Cell

    Proteomics 2006;5:1840-52.

    2- Poon LL, Wong BWY, Ma EHT et al. Sensitive and inexpensive molecular test

    for falciparum malaria: detecting Plasmodium falciparum DNA directly from

    heat-treated blood by loop-mediated isothermal amplification. Clin Chem

    2006;52:303-6.

    3- Benlloch S, Galbis-Caravajal JM, Martín C et al. Potential diagnostic value of

    methylation profile in pleural fluid and serum from cancer patients with pleural

    effusion. Cancer 2006;107:1859-65.

    4- Ward DG, Cheng Y, N'Kontchou C et al. Changes in the serum proteome

    associated with the development of hepatocellular carcinoma in hepatitis C-

    related cirrhosis. Br J Cancer 2006; 94:287-292.

    5- Grote HJ, Schmiemann V, Geddert H et al. Methylation of RAS association

    domain family protein 1A as a biomarker of lung cancer. Cancer 2006;108:129-

    34.

    6- Kern W, Kohlman A, Schoch C et al. Comparison of mRNA abundance

    quantified by gene expression profiling and percentage of positive cells using

    immunophenotyping for diagnostic antigens in acute and chronic leukemias.

    Cancer 2006;107:2401-7.

    7- Florent M, Kasahian S, Vekhoff A et al. Prospective Evaluation of a Polymerase

    Chain ReactionELISA Targeted to Aspergillus fumigatus and Aspergillus

    flavus for the Early Diagnosis of Invasive Aspergillosis in Patients with

    Hematological Malignancies. J Infec Dis 2006;193:741-7.

    8- Dawson ED, Moore C, Smagala JA et al. MChip: A Tool for Influenza

    Surveillance. Anal Chem 2006;78:7610-5.

    9- Meyer-Monard S, Parlier V, Passweg J et al. Combination of broad molecular

    screening and cytogenetic analysis for genetic risk assignment and diagnosis in

    patients with acute leucemia. Leukemia 2006;20:247-53.

    10- Scarlett CJ, Smith RC, Saxby A et al. Proteomic Classification of Pancreatic

    Adenocarcinoma Tissue Using Protein Chip Technology. Gastroenterology

    2006;130:1670-8.

    11- Theodorescu D, Wittke S, Ross MM et al. Discovery and validation of new

    protein biomarkers for urothelial cancer: a prospective analysis. Lancet Oncol

    2006;7:230-40.

    12- Agranoff D, Fernandez-Reyes D, Papadopoulos MC et al. Identification of

    diagnostic markers for tuberculosis by fingerprinting of serum. Lancet

    2006;368:1012-21.

    13- Srinivasan R, Daniels J, Fusaro V et al. Accurate diagnosis of acute graft versus

    host disease using serum proteomic pattern analysis. Exp Hematol 2006;34:796-

    801.

    14- Hye A, Lynham S, Thambisetty M et al. Proteome-based plasma biomarkers for

    Alzheimer's disease. Brain 2006;129: 3042-50.

    15- Guillaud M, Benedet JL, Cantor SB, Staerkel G, Follen M, MacAulay C. DNA

    ploidy compared with Human Papilloma virus testing and conventional cervical

    cytology as a primary screening test for cervical high grade lesions and cancer in

    1555 patients with biopsy confirmation. Cancer 2006;107:309-18. 16- Mosley K, Tam FWK, Edwards RJ, Crozier J, Pusey CD, Lightstone L. Urinary

    proteomic profiles distinguish between active and inactive lupus nephritis.

    Rheumatology 2006;45:1497-504.

    17- Shi Q, Harris LN, Lu X et al. Declining plasma fibrinogen alpha fragment

    identifies HER2-positive breast cancer patients and reverts to normal levels after

    surgery. J Proteome Res 2006;5:2947-55.

    18- Holloway AJ, Diyagama DS, Opeskin K et al. A molecular diagnostic test for

    distinguishing lung adenocarcinoma from malignant mesothelioma using cells

    collected from pleural effusions. Clin Cancer Res 2006;12:5129-35. 19- Poon TCW, Sung JJY, Chow SM et al. Diagnosis of Gastric cancer by serum

    proteomic fingerprinting. Gastroenterology 2006;130:1858-64. 20- Ward DG, Suggett N, Cheng Y et al. Identification of serum biomarkers for

    colon cancer by proteomic analysis. Br J Cancer 2006;94:1898-905. 21- Paterson PJ, Seaton S, McHugh TD et al. Validation and clinical application of

    Molecular methods for the identification of Molds in Tissue. Clin Infect Dis

    2006;42:51-6.

    22- Tester DJ, Will MS, Haglund CM, Ackerman MJ. Effect of clinical phenotype

    on yield of long QT syndrome genetic testing. J Am Coll Cardiol 2006;47:764-8.

    23- Pasinetti GM, Unger LH, Lange DJ et al. Identification of potential CSF

    biomarkers in ALS. Neurology 2006;66:1218-22.

    24- Zhou Y, Lum JMS, Yeo GH, Kiing J, Tay SKT, Chong SS. Simplified

    molecular diagnosis of fragile X syndrome by fluorescent methylation-specific

    PCR and GeneScan analysis. Clin Chem 2006;52:1492-500. 25- Procter M, Chou LS, Tang W, Jama M, Mao R. Molecular diagnosis of Prader-

    Willi and Angelman syndromes by methylation-specific melting analysis and

    methylation-specific multiplex ligation-dependent probe amplification. Clin

    Chem 2006;52:1276-83.

    26- Alsmadi OA, Al-Kayal F, Al-Hamed M, Meyer BF. Frequency of common HFE

    variants in the Saudi population: a high throughput molecular beacon-based

    study. BMC Med Genet 2006;7:43.

    27- Yannaraki M, Rebibou JM, Ducloux D et al. Urinary cytotoxic molecular

    markers for a noninvasive diagnosis in acute renal transplant rejection. Transpl

    Int 2006;19:759-68.

    28- Ren H, Du N, Liu G et al. Analysis of variabilities of serum proteomic spectra

    in patients with gastric cancer before and after operation. World J Gastroenterol

    2006;12:2789-92.

    29- Liang Y, Fang M, Li J et al. Serum proteomic patterns for gastric lesions as

    revealed by SELDI mass spectrometry. Exp Mol Pathol 2006;81:176-80. 30- Li X, Miyajima M, Mineki R, Taka H, Murayama K, Ari H. Analysis of

    potential diagnostic biomarkers in cerebrospinal fluid of idiopathic normal

    pressure hydrocephalus by proteomics. Acta Neurochir (Wien) 2006;148:859-64. 31- Zhou L, Cheng L, Tao L, Jia X, Lu Y, Liao P. Detection of hypopharyngeal

    squamous cell carcinoma using serum proteomics. Acta Oto-laryngol

    2006;126:853-60.

    32- Satiroglu-Tufan NL, Tufan AC, Semerci CN, Bagci H. Accurate diagnosis of a

    homozygous G1138A mutation in the fibroblast growth factor receptor 3 gene

    responsible for achondroplasia. Tohoku J Exp Med 2006;208:103-7. 33- Zhu LR, Zhang WY, Yu L, Zhang JZ, Liao QP. Serum proteomic features for

    detection of endometrial cancer. Int J Gynecol Cancer 2006;16:1374-8. 34- Lin YW, Lai HC, Lin CY et al. Plasma proteomic profiling for detecting and

    differentiating in situ and invasive carcinomas of the uterine cervix. Int J

    Gynecol Cancer 2006;16:1216-24.

    35- Hewitt MJ, Wood N, Quinton ND et al. The detection of microsatellite

    instability in blind endometrial samples--a potential novel screening tool for

    endometrial cancer in women from hereditary nonpolyposis colorectal cancer

    families? Int J Gynecol Cancer 2006;16:1393-400.

    36- German HNPCC consortium, Müller A, Beckmann C et al. Prevalence of the

    mismatch-repair-deficient phenotype in colonic adenomas arising in HNPCC

    patients: results of a 5-year follow-up study. Int J Colorectal Dis 2006;21:632-

    41.

    37- Krause CH, Eastick K, Ogilvie MM. Real-time PCR for mumps diagnosis on

    clinical specimens--comparison with results of conventional methods of virus

    detection and nested PCR. J Clin Virol 2006;37:184-9.

    38- Antonishyn NA, Crozier NA, McDonald RR, Levett PN, Horsman GB. Rapid

    detection of Norovirus based on an automated extraction protocol and a real-

    time multiplexed single-step RT-PCR. J Clin Virol 2006;37:156-61. 39- Wang YC, Hsu HS, Chan TP, Chan JT. Molecular diagnostic markers for lung

    cancer in sputum and plasma. Ann NY Acad Sci 2006;1075:179-84. 40- Papadopoulou E, Davilas E, Sotiriou V et al. Cell-free DNA and RNA in

    plasma as a new molecular marker for prostate and breast cancer. Ann NY Acad

    Sci 2006;1075:235-43.

    41- Burczynski ME, Peterson RL, Twine NC et al. Molecular classification of

    Crohn‟s disease and Ulcerative colitis patients using transcriptional profiles in

    peripheral blood mononuclear cells. J Mol Diagn 2006;8:51-61. 42- Chen YF, Kou PL, Tsai SJ et al. Computational analysis and refinement of

    sequence structure on chromosome 22q11.2 region: application to the

    development of quantitative real-time PCR assay for clinical diagnosis.

    Genomics 2006;87:290-7.

    43- Townsend MB, Dawson ED, Mehlmann M et al. Experimental Evaluation of

    the FluChip diagnostic microarray for influenza virus surveillance. J Clin

    Microbiol 2006;44:2863-71.

    44- Franco-Álvarez de Luna F, Ruiz P, Gutiérez J, Casal M. Evaluation of the

    GenoType Mycobacteria Direct assay for detection for mycobacterium

    tuberculosis complex and four atypical mycobacterium species in clinical

    simples. J Clin Microbiol 2006;44:3025-7.

    45- Deborggraeve S, Claes F, Laurent T et al. Molecular Dipstick Test for diagnosis

    of sleeping sickness. J Clin Microbiol 2006;44:2884-9.

    46- Scarlett CJ, Saxby AJ, Neilson AQ et al. Proteomic profiling of

    cholangiocarcinoma: diagnostic potential of SELDI-TOF MS in malignant bile

    stricture. Hepatology 2006;44:658-66.

    47- Wu SP, Lin YW, Lai HC, Chu TY, Kuo YL, Liu HS. SELDI-TOF MS profiling

    of plasma proteins in ovarian cancer. Taiwan J Obstet Gynecol 2006;45:26-32. 48- Van Werkhoven MA, Thorburn DR, Gedeon AK, Pitt JJ. Monolysocardiolipid

    in cultured fibroblasts is a sensitive and specific marker for Barth Syndrome. J

    Lipid Res 2006;47:2346-51.

    49- Aulicino PC, Carrillo MG, Kopka J, Mangano AM, Ovejero M, Sen L. HIV-1

    Genetic diversity in Argentina and early diagnosis of perinatal infection.

    Medicina (B Aires) 2006;66:319-26.

    50- Jordan JA, Durso MB, Butchko AR, Jones JG, Brozanski BS. Evaluating the

    Near-term infant for early onset sepsis. J Mol Diagn 2006;8:357-63. 51- Talantov D, Baden J, Jatkoe T et al. A quantitative reverse transcriptase

    polymerase chain reaction assay to identify metastatic carcinoma tissue of origin.

    J Mol Diagn 2006;8:320-9.

    52- Murphy KM, Zhang S, Geiger T et al. Comparison of the microsatellite

    instability analysis system and the Bethesda panel for the determination of

    Microsatellite instability in colorectal cancer. J Mol Diagn 2006;8:305-11. 53- Falk M, Vojtísková M, Lukás Z, Kroupová I, Froster U. Simple procedure for

    automatic detection of unstable alleles in the myotonic dystrophy and

    Huntington's disease loci. Genet Test 2006;10:85-97.

    54- Jenkins C, Tembo M, Chart H et al. Detection of enteroaggregative Escherichia

    coli in faecal samples from patients in the community with diarrhoea. J Med

    Microbiol 2006;55:1493-7.

    55- Bhattacharyya S, Epstein J, Suva LJ. Biomarkers that discriminate multiple

    myeloma patients with or without skeletal involvement detected using SELDI-

    TOF mass spectrometry and statistical and machine learning tools. Dis Markers

    2006;22:245-55.

    56- Abdi F, Quinn JF, Jankovic J et al. Detection of biomarkers with a multiplex

    quantitative proteomic platform in cerebrospinal fluid of patients with

    neurodegenerative disorders. J Alzheimers Dis 2006;9:293-348.

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