Browsing by Subject "SPECIMENS"

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  • Merkkola-von Schantz, Paivi A.; Kauhanen, Susanna M. C.; Jahkola, Tiina A.; Krogerus, Leena; Hukkinen, Katja S. (2017)
    Background The role of preoperative imaging and the usability of different imaging modalities is highly variable and controversial in reduction mammaplasty patients. Our study describes the imaging process in a single center in regard to modality selection, age and timing, and of the association between imaging and histopathological findings in reduction mammaplasty specimens. Methods Nine hundred eighteen women, who underwent reduction mammaplasty during 1.1.2007-31.12.2011, were retrospectively reviewed for demographics, preoperative imaging, further preoperative examinations, and pathology reports. Results Preoperative imaging had been conducted for 89.2% (n = 819) of the patients. In 49 (6.0%) patients, suspicious preoperative imaging led to further examinations revealing 2 high-risk lesions (atypical ductal hyperplasia (ADH), lobular carcinoma in situ (LCIS)), and 2 cancers preoperatively. Postoperatively abnormal histopathology specimens were revealed in 88 (10.4%) patients. The incidence of high-risk lesions was 5.5% (n = 47), and the incidence of cancer was 1.2% (n = 10). Preoperative imaging was normal (BI-RADS 1 and BI-RADS 2) in 80.8% of these patients. The sensitivity of the preoperative imaging for cancer detection was 20.0%, and the specificity was 100.0%. Conclusions Preoperative imaging and further examinations do not sufficiently detect malignant or cancer risk-increasing findings. Therefore, histopathological analysis of reduction mammaplasty specimens seems mandatory.
  • Almangush, Alhadi; Youssef, Omar; Pirinen, Matti; Sundström, Jari; Leivo, Ilmo; Mäkitie, Antti A. (2019)
    Tumour budding has emerged as a promising prognostic marker in many cancers. We systematically reviewed all studies that evaluated tumour budding in diagnostic biopsies. We conducted a systematic review of PubMed, MEDLINE, Scopus, Web of Science and Cochrane library for all articles that have assessed tumour budding in diagnostic (i.e. pretreatment or pre-operative) biopsies of any tumour type. Two independent researchers screened the retrieved studies, removed duplicates, excluded irrelevant studies and extracted data from the eligible studies. A total of 13 reports comprising 11 cohorts were found to have studied tumour budding in diagnostic biopsies. All these reports showed that evaluation of tumour budding in diagnostic biopsies was easily applicable. A strong association was observed between tumour budding score in diagnostic biopsies and corresponding surgical samples. Evaluation of tumour budding in diagnostic biopsies had a significant prognostic value for lymph node metastasis and patient survival. In all studies, tumour budding was a valuable marker of tumour aggressiveness and can be evaluated in technically satisfactory diagnostic biopsies. Thus, the assessment of tumour budding seems to identify the behaviour of cancer, and therefore to facilitate treatment planning.
  • Gauthier, Jérémy; Pajkovic, Mila; Neuenschwander, Samuel; Kaila, Lauri; Schmid, Sarah; Orlando, Ludovic; Alvarez, Nadir (2020)
    Erosion of biodiversity generated by anthropogenic activities has been studied for decades in many areas at species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.
  • Twort, Victoria G.; Minet, Joël; Wheat, Christopher W.; Wahlberg, Niklas (2021)
    Museomics is a valuable approach that utilizes the diverse biobanks that are natural history museums. The ability to sequence genomes from old specimens has expanded not only the variety of interesting taxa available to study but also the scope of questions that can be investigated in order to further knowledge about biodiversity. Here, we present whole genome sequencing results from the enigmatic genus Whalleyana (comprising two species - occurring in drier biomes of Madagascar - previously placed in a monotypic superfamily, Whalleyanoidea), as well as from certain species of the families Callidulidae and Hyblaeidae (Calliduloidea and Hyblaeoidea, respectively). Library preparation was carried out on four museum specimens and one existing DNA extract and sequenced with Illumina short reads. De novo assembly resulted in highly fragmented genomes with the N50 ranging from 317 to 2078 bp. Mining of a manually curated gene set of 331 genes from these draft genomes had an overall gene recovery rate of 64-90%. Phylogenetic analysis places Whalleyana as sister to Callidulidae and Hyblaea as sister to Pyraloidea. Since the former sister-group relationship turns out to be also supported by ten morphological synapomorphies, we propose to formally assign the Whalleyanidae to the superfamily Calliduloidea. These results highlight the usefulness of not only museum specimens but also existing DNA extracts, for whole genome sequencing and gene mining for phylogenomic studies.
  • Merkkola-von Schantz, Paivi A.; Jahkola, Tiina A.; Krogerus, Leena A.; Kauhanen, Susanna M. C. (2017)
    Introduction: Contralateral reduction mammaplasty is regularly included in the treatment of breast cancer patients. We analyzed the incidence of occult breast cancer and high-risk lesions in reduction mammaplasty specimens of women with previous breast cancer. We also analyzed if timing of reduction mammaplasty in relation to oncological treatment influenced the incidence of abnormal findings, and compared if patients with abnormal contralateral histopathology differed from the study population in terms of demographics. Materials and methods: The study consisted of 329 breast cancer patients, who underwent symmetrizing reduction mammaplasty between 1/2007 and 12/2011. The data was retrospectively analyzed for demographics, operative and histopathology reports, oncological treatment, and postoperative follow-up. Results: Reduction mammaplasty specimens revealed abnormal findings in 68 (21.5%) patients. High-risk lesions (ADH, ALH, and LCIS) were revealed in 37 (11.7%), and cancer in six (1.9%) patients. Abnormal histopathology correlated with higher age (p = 0.0053), heavier specimen (p = 0.0491), and with no previous breast surgery (p <0.001). Abnormal histopathological findings were more frequent in patients with reduction mammaplasty performed prior to oncological treatment (p <0.001), and in patients with immediate reconstruction (p = 0.0064). Conclusion: The incidences of malignant and high-risk lesions are doubled compared to patients without prior breast cancer. Patients with abnormal histopathology cannot be preoperatively identified based on demographics. If reduction mammaplasty is performed before oncological treatment, the incidence of abnormal findings is higher. In the light of our results, contralateral reduction mammaplasty with histopathological evaluation in breast cancer patients offers a sophisticated tool to catch those patients whose contralateral breast needs increased attention. (C) 2017 Elsevier Ltd. All rights reserved.
  • Virtanen, Anni; Anttila, Ahti; Nieminen, Pekka (2015)
    Background: Offering self-sampling to non-attendees of cervical screening increases screening attendance. Methods: We used observations from two Finnish studies on the use of self-sampling among the non-attendees to estimate in a hypothetical screening population of 100,000 women the possible costs per extra screened woman and costs per extra detected and treated CIN2+ with three intervention strategies; 1) a primary invitation and a reminder letter, 2) a primary invitation and a mailed self-sampling kit and 3) two invitation letters and a self-sampling kit. The program costs were derived from actual performance and costs in the original studies and a national estimate on management costs of HPV related diseases. Results: The price per extra participant and price per detected and treated CIN2+ lesion was lower with a reminder letter than by self-sampling as a first reminder. When self-sampling was used as a second reminder with a low sampler price and a triage Pap-smear as a follow-up test for HPV-positive women instead of direct colposcopy referral, the eradication of a CIN2+ lesion by self-sampling was not more expensive than in routine screening, and the addition of two reminders to the invitation protocol did not increase the price of an treated CIN2+ lesion in the entire screened population. Conclusions: As a first reminder, a reminder letter is most likely a better choice. As second reminder, the higher costs of self-sampling might be compensated by the higher prevalence of CIN2+ in the originally non-attending population.