Abstract The study of rare paediatric brain tumours is significantly constrained by limited sample availability, hindering large-scale molecular characterisation and advances in diagnosis and treatment. Long-term biobanking offers a powerful solution by enabling access to archival tumour material collected over decades, thereby expanding cohort size and diversity. Formalin-fixed paraffin-embedded (FFPE) tissue represents the most abundant and stable source of paediatric brain tumour specimens and remains a critical resource for generating genomic and epigenomic data. Here, we leverage a unique FFPE brain tumour biobank comprising specimens collected over the past 80 years at the Women’s and Children’s Hospital (South Australia). This collection includes a broad spectrum of paediatric brain tumours, spanning low-grade to high-grade malignancies and multiple rare tumour entities. However, the age and variable preservation quality of archival FFPE samples present significant technical challenges for modern molecular profiling. This study focuses on optimising multi-omics workflows for archival FFPE tissue, including genomic DNA extraction, DNA library preparation, and downstream analysis. We demonstrate that sample-specific optimisation of extraction and library preparation protocols is essential to achieve sufficient DNA yield and quality, particularly for older FFPE specimens. Pooling DNA extracted from multiple tumour regions within individual cases was critical for meeting minimal input requirements in older samples. Using DNA methylation profiling, we show that archival tumours can be reclassified with greater molecular precision compared to historical histopathological diagnoses. In several cases, methylation-based classification refined tumour subtypes or identified previously unclassifiable tumours, highlighting discrepancies between morphology-based and molecular diagnoses. Our findings demonstrate that advanced multi-omics approaches can be successfully applied to decades-old FFPE paediatric brain tumour samples, unlocking valuable biological and diagnostic insights. This work underscores the importance of archival biobanks in paediatric neuro-oncology and further supports the integration of molecular profiling into diagnostic frameworks to improve tumour classification, risk stratification, and ultimately patient care.

PTEN hamartoma tumour syndrome (PHTS) is a rare cancer predisposition syndrome, caused chiefly by pathogenic and likely pathogenic (P/LP) variants in in the PTEN gene. Carriers have substantially elevated risks of various malignancies and develop benign lesions in multiple organ systems. The rarity of this disease, the decades-long unfolding of its clinical features, involvement of multiple sites and the absence of distinguishing features of each lesion hamper the identification of this condition, limiting opportunities for screening of affected individuals and their families. Given laboratory information systems are the repositories of patients' biopsies, we are interested in whether PHTS patients' prior biopsies may serve as clues to the possibility of this syndrome. With ethics committee approval, through a collaboration amongst our state-wide Adult Genetics Unit and all pathology laboratories in our state, we have undertaken a 28-year longitudinal survey (1990-2018) of the biopsy histories of 12 women known to have P/LP PTEN variants. Only one woman had a family history of Cowden syndrome, with the remaining 11 patients' mutations being discovered later. The earliest biopsy was at age 19. The most common finding was the development of multiple benign mucocutaneous lesions, with 10 women presenting with these, including a range of benign vascular lesions (eight patients), various fibromatous lesions of the skin and mucosal sites (six patients), a ganglioneuroma and a juvenile polyp. Ten women developed breast cancer, only four before the age of 40. Seven women developed a second breast cancer, two synchronously and five at intervals of 3-11 years. Other neoplasms included endometrial carcinoma (two patients) and dysplastic cerebellar gangliocytoma (three patients). Integrating the biopsy histories of PTEN P/LP variant carriers over time may assist in raising the possibility of an underlying cancer susceptibility syndrome, so appropriate clinical and genetic counselling and evaluation may be considered.

PTEN hamartoma tumour syndrome (PHTS) is an autosomal dominant hereditary cancer syndrome, caused mostly by germline pathogenic variants in PTEN. Female carriers have an up to 80% lifetime risk of breast cancer. Pathological features of breast cancer in PHTS have seldom been reported. In a collaboration between all histopathology laboratories in our state and our statewide familial cancer service, we tracked the breast biopsies of 12 females with known PTEN pathogenic or likely pathogenic (P/LP) variants (January 1990 to January 2018). Two further cases were added by a Victorian cancer genetics unit. Breast cancer, inclusive of invasive cancer or ductal carcinoma in situ (DCIS), was diagnosed in 12 of 14 cases (85.7%). One case had a family history of PHTS, and six had a family history of breast cancer. The mean age at first breast cancer diagnosis was 41.6 years (range 27-63). Six cases developed more than one breast cancer. Five (42%) developed contralateral breast cancer. Ten of the 12 invasive cancers were of no special type, and two were reported as lobular carcinomas. None were grade 1. When reported, all cancers were hormone-receptor positive and HER2 negative. All were associated with DCIS. The DCIS spanned all grades. The two cases without breast cancer still required surgery for exuberant benign changes, including papillomas, fibroadenomatoid change, florid ductal epithelial hyperplasia, adenosis and stromal fibrosis. We note that the morphology and receptor profiles of breast cancer in individuals with P/LP PTEN variants are not distinctive. Contrary to prevalent beliefs, these cancers do not conform to the contemporary definition of apocrine breast carcinoma. Greater familiarity of healthcare professionals with the overall clinical and pathological findings in PHTS and the validated Cleveland Clinic PTEN calculator (http://www.lerner.ccf.org/gmi/ccscore) would improve the recognition of female PHTS individuals with breast cancer. Earlier identification of their cancer predisposition syndrome would benefit these patients and their families who are at high risk of a range of cancers.

Pregnancy loss and perinatal death are devastating events for families. We assessed 'genomic autopsy' as an adjunct to standard autopsy for 200 families who had experienced fetal or newborn death, providing a definitive or candidate genetic diagnosis in 105 families. Our cohort provides evidence of severe atypical in utero presentations of known genetic disorders and identifies novel phenotypes and disease genes. Inheritance of 42% of definitive diagnoses were either autosomal recessive (30.8%), X-linked recessive (3.8%) or autosomal dominant (excluding de novos, 7.7%), with risk of recurrence in future pregnancies. We report that at least ten families (5%) used their diagnosis for preimplantation (5) or prenatal diagnosis (5) of 12 pregnancies. We emphasize the clinical importance of genomic investigations of pregnancy loss and perinatal death, with short turnaround times for diagnostic reporting and followed by systematic research follow-up investigations. This approach has the potential to enable accurate counseling for future pregnancies.

Perinatal death, of a fetus or newborn, is a devastating event for families. Following nationwide multicentre recruitment, we assessed ‘genomic autopsy’ as an adjunct to standard autopsy for 200 families who experienced perinatal death, and provided a definite or candidate genetic diagnosis in 105 families. From this understudied cohort, half of the (candidate) diagnoses were phenotype expansions or novel disease genes, revealing previously unknown in-utero presentations of existing developmental disorders, and genomic disorders that are likely incompatible with life. Among the definite diagnoses, 43% were recessively or dominantly inherited, posing a 25% or 50% recurrence risk for future pregnancies. Ten families used their diagnosis for preimplantation or prenatal diagnosis of 12 pregnancies, facilitating the delivery of ten healthy newborns and management of two affected pregnancies. We emphasize the clinical importance of genomic investigations of perinatal death, with short turn-around times, enabling accurate counselling and options for families to prevent recurrence.

Inflammatory myofibroblastic tumours (IMTs) are rare soft tissue tumours. Reports of gastrointestinal tract, liver and pancreas tumours are limited. The objective of this study is to identify presenting features, contributing prognostic / etiological factors and any variability in outcomes in the context of different historical treatments. We retrospectively reviewed the records of seven children treated at our hospital between 2006 and 2019 and assessed the demographic, presentation, treatment, immunohistochemistry, and outcomes of their tumours. Age range at presentation was 4 months-15 years with a male predominance. Presentations were typically due to local mass effect or incidental discovery. Systemic symptoms were rare. Outcomes were good with six out of seven stable or in remission irrespective of treatment. Surgical resection where possible is the treatment of choice. Medical therapy had good outcomes with chemotherapy acting as first line treatment when required. The only negative prognostic factor identified was local spread at the time of presentation.

Congenital abnormalities and infections are the predominant cause of perinatal death in developed countries. While standard-of-care autopsy investigations can ascertain the event that caused the death, the aetiology cannot always be established. Genetic approaches have demonstrated utility in identifying the underlying causes of congenital anomalies and infectious diseases, but the feasibility of simultaneous metagenomic and genomic analyses has not been examined. To determine the potential of this consolidated approach, genome sequencing was performed on DNA from lung in 20 cases of fetal death. Causative microbes were correctly identified in 4/7 known infection cases and plausible causative microbes identified for 2/5 cases unresolved from standard investigations. No significant microbial load was identified in 8/8 cases due to congenital abnormality. While methods for concurrent human and microbial genome analyses still require optimisation, this dual approach should improve the diagnostic yield compared to current standard-of-care investigations, enabling more accurate counselling and appropriate care in subsequent pregnancies.

Background Periventricular nodular heterotopia (PNH) is a malformation of cortical development characterized by nodules of abnormally migrated neurons. The cause of posteriorly placed PNH is not well characterised and we present a case that provides insights into the cause of posterior PNH. Case presentation We report a fetus with extensive posterior PNH in association with biallelic variants in LAMC3 . LAMC3 mutations have previously been shown to cause polymicrogyria and pachygyria in the occipital cortex, but not PNH. The occipital location of PNH in our case and the proposed function of LAMC3 in cortical development suggest that the identified LAMC3 variants may be causal of PNH in this fetus. Conclusion We hypothesise that this finding extends the cortical phenotype associated with LAMC3 and provides valuable insight into genetic cause of posterior PNH.

Autosomal dominant (de novo) mutations in PBX1 are known to cause congenital abnormalities of the kidney and urinary tract (CAKUT), with or without extra-renal abnormalities. Using trio exome sequencing, we identified a PBX1 p.(Arg107Trp) mutation in a deceased one-day-old neonate presenting with CAKUT, asplenia, and severe bilateral diaphragmatic thinning and eventration. Further investigation by droplet digital PCR revealed that the mutation had occurred post-zygotically in the father, with different variant allele frequencies of the mosaic PBX1 mutation in blood (10%) and sperm (20%). Interestingly, the father had subclinical hydronephrosis in childhood. With an expected recurrence risk of one in five, chorionic villus sampling and prenatal diagnosis for the PBX1 mutation identified recurrence in a subsequent pregnancy. The family opted to continue the pregnancy and the second affected sibling was stillborn at 35 weeks, presenting with similar severe bilateral diaphragmatic eventration, microsplenia, and complete sex reversal (46, XY female). This study highlights the importance of follow-up studies for presumed de novo and low-level mosaic variants and broadens the phenotypic spectrum of developmental abnormalities caused by PBX1 mutations.

ANZ Journal of SurgeryVolume 87, Issue 1-2 p. 98-100 IMAGES FOR SURGEONS Spindle cell haemangioma mimicking a popliteal aneurysm Jeremy Granger MBBS, BAppSc, Jeremy Granger MBBS, BAppSc Department of Paediatric Surgery, Women's and Children's Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorNick Manton MBBS, BMedSci, FRCPA, Nick Manton MBBS, BMedSci, FRCPA Department of Pathology, Women's and Children's Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorMark Hamilton BHB, MBChC, FRACS, Mark Hamilton BHB, MBChC, FRACS Department of Vascular Surgery, The University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorJoseph Dawson MBBS, MRCS, MD, ChM, FRCS, Joseph Dawson MBBS, MRCS, MD, ChM, FRCS Department of Vascular Surgery, The University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this author Jeremy Granger MBBS, BAppSc, Jeremy Granger MBBS, BAppSc Department of Paediatric Surgery, Women's and Children's Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorNick Manton MBBS, BMedSci, FRCPA, Nick Manton MBBS, BMedSci, FRCPA Department of Pathology, Women's and Children's Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorMark Hamilton BHB, MBChC, FRACS, Mark Hamilton BHB, MBChC, FRACS Department of Vascular Surgery, The University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this authorJoseph Dawson MBBS, MRCS, MD, ChM, FRCS, Joseph Dawson MBBS, MRCS, MD, ChM, FRCS Department of Vascular Surgery, The University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, AustraliaSearch for more papers by this author First published: 29 September 2014 https://doi.org/10.1111/ans.12861Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. References 1 Weiss SW, Enzinger FM. Spindle cell hemangioendothelioma: a low-grade angiosarcoma resembling a cavernous hemangioma and Kaposi's sarcoma. Am. J. Surg. Pathol. 1986; 10: 521– 30. 2 Weiss SW, Perkins P. Spindle cell hemangioendothelioma: an analysis of 78 cases with reassessment of its pathogenesis and biologic behaviour. Am. J. Surg. Pathol. 1996; 20: 1196– 204. 3 Fukunaga M, Ushigome S, Nikaido T, Ishikawa E, Nakamori K. Spindle cell hemangioma: an immunohistochemical and flow cytometric study of six cases. Pathol. Int. 1995; 45: 589– 95. 4 Terashi H, Itami S, Kurata S, Sonoda T, Takayasu S, Yokoyama S. Spindle cell hemangioendothelioma: report of three cases. J. Dermatol. 1991; 18: 104– 11. Volume87, Issue1-2January/February 2017Pages 98-100 ReferencesRelatedInformation

Background: Fluorine-18-2-fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET) is frequently used in the diagnosis of tumors, including colorectal cancer (CRC).This study aimed to determine whether PET could be used to detect CRC and colorectal adenomas, with endoscopic and pathologic confirmation.Methods: The PET results were verified by colonoscopy.Patients who underwent total colonoscopy (TCS) and PET between October 2002 and September 2012 at a tertiary cancer center were evaluated.TCS and PET were performed independently within 1 year.Cases of diminutive polyps (1-5 mm) were not included.Advanced CRC was defined as tumor extending into the muscularis propria or deeper, corresponding to T2-T4 stages according to TNM classification.Early-stage CRC was defined as tumors invading within submucosal layer, corresponding to Tis and T1 stages.Excluding advanced CRC, lesions were classified according to morphology as flat, depressed, or protruded.PET and PET-CT images were reviewed by at least 2 board-certified radiologists.Focal FDG uptake was determined in each portion of the colon (cecum and ascending, transverse, descending, and sigmoid colon) and rectum.FDG uptake in a matched segment containing a lesion was defined as a true positive result.Cases with a previous history of colorectal resection, direct invasion or peritoneum dissemination of other cancers, hyperglycemia (>150 mg/dl), incomplete TCS, hereditary colon cancer, preceding therapy, and anal canal tumors were excluded.To clarify the detectability of adenoma and CRC, nonepithelial tumors were excluded.Results: We identified 2483 consecutive eligible patients.A total of 694 lesions, 6 mm or larger, were detected by TCS: 205 advanced CRCs, 132 earlystage CRCs, and 357 adenomas.Of the 694 lesions that were 6 mm or larger, 374 (53.9%) were PET positive.Of the 531 cases with positive FDG uptake, 374 (70.4%) had lesions detected in the matched segments.False positive, which was defined as no or trivial findings despite of significant FDG uptake, was 157 (29.6%).Sensitivities of PET for advanced CRC, early-stage CRC, and adenoma were 98%, 69%, and 23%, respectively.Table1 summarizes the sensitivities of PET stratified by tumor pathology and size.The increase in sensitivity correlated with lesion size and tumor grade.The sensitivity was nearly 50% for small (6-9 mm) early-stage CRCs.PET was able to detect approximately 40% of large adenomas (10-19 mm in size); however, its sensitivity for small adenomas (6-9 mm) decreased to 10%.Regarding morphology, PET was significantly less sensitive for flat lesions than for depressed or protruded lesions (p < 0.001).Conclusions: The sensitivity of PET in diagnosis of CRC stratified by lesion size, pathology, and morphology was evaluated.PET had an acceptable sensitivity for early-stage CRCs and large adenomas.Table1.PET sensitivity stratified by lesion size and pathology (95% confidence interval) Su1250

Aim To evaluate the usefulness of microarray in fetal autopsy cases with or without malformations. Introduction Microarrays were performed as part of autopsy investigation on 90 cases, including stillbirths, fetuses that died in utero or were terminated due to abnormal ultrasound findings between February 2009 and September 2011. Methods Microarray was performed using the BlueGnome Cyto-chip oligo ISCA 60K array platform. Microarray results and autopsy reports of all cases were reviewed to determine the presence of any fetal malformations and to categorise the positive microarray findings as causative, of unknown clinical significance or not causative. The number of causative findings identified by microarray in cases with at least one malformation was compared to the number of causative findings identified in cases without any malformations. Results Five microarrays failed. Of the remaining 85 cases with microarray results, 53 cases had at least one malformation and 32 cases had no malformation. Four cases (7.5%) with one or more malformations had a causative finding on microarray, compared to no cases without any malformations. Conclusions Microarray is a valuable investigation in fetal autopsy cases with at least one malformation, but not for those without any malformation. To evaluate the usefulness of microarray in fetal autopsy cases with or without malformations.