Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases.

BACKGROUND: Targeted Next Generation Sequencing is a common and powerful approach used in both clinical and research settings. However, at present, a large fraction of the acquired genetic information is not used since pathogenicity cannot be assessed for most variants. Further complicating this scenario is the increasingly frequent description of a poli/oligogenic pattern of inheritance showing the contribution of multiple variants in increasing disease risk. We present an approach in which the entire genetic information provided by target sequencing is transformed into binary data on which we performed statistical, machine learning, and network analyses to extract all valuable information from the entire genetic profile. To test this approach and unbiasedly explore the presence of recurrent genetic patterns, we studied a cohort of 112 patients affected either by genetic Creutzfeldt-Jakob (CJD) disease caused by two mutations in the PRNP gene (p.E200K and p.V210I) with different penetrance or by sporadic Alzheimer disease (sAD). RESULTS: Unsupervised methods can identify functionally relevant sources of variation in the data, like haplogroups and polymorphisms that do not follow Hardy-Weinberg equilibrium, such as the NOTCH3 rs11670823 (c.3837 + 21 T > A). Supervised classifiers can recognize clinical phenotypes with high accuracy based on the mutational profile of patients. In addition, we found a similar alteration of allele frequencies compared the European population in sporadic patients and in V210I-CJD, a poorly penetrant PRNP mutation, and sAD, suggesting shared oligogenic patterns in different types of dementia. Pathway enrichment and protein-protein interaction network revealed different altered pathways between the two PRNP mutations. CONCLUSIONS: We propose this workflow as a possible approach to gain deeper insights into the genetic information derived from target sequencing, to identify recurrent genetic patterns and improve the understanding of complex diseases. This work could also represent a possible starting point of a predictive tool for personalized medicine and advanced diagnostic applications.

Severe laryngeal fracture treated by supracricoid laryngectomy.

OBJECTIVE: To report a rare case of severe laryngeal fracture treated by supracricoid laryngectomy. Previously, a few cases of major laryngeal trauma treated by reconstructive laryngectomy have been briefly described. This paper aims to comprehensively document a rare case of severe laryngeal fracture for which this difficult treatment choice represented an acceptable option. METHODS: A 33-year-old woman sustained very serious blunt laryngeal trauma. The complexity of the laryngeal injuries led us to opt for supracricoid laryngectomy, rather than to attempt laryngeal repair. RESULTS: The post-operative course was normal. The patient's post-operative voice was breathy but functional. No airway stenoses occurred. CONCLUSION: For severe laryngeal fractures, reparative procedures and stenting constitute the standard treatment. However, in selected and especially critical cases, a primary partial or reconstructive laryngectomy is justifiable.

Congenital dacryocystocele: diagnosis and treatment.

Five children were diagnosed with congenital dacryocystocele; in all cases, the cystic lesion was unilateral; age ranged from 7 to 60 days (mean 29 days). The mean ultrasonography diameter of the cyst, at the time of the diagnosis, was 11.51 mm. Topical and systemic antibiotics and massage were prescribed. One patient had no recurrence of the dacryocystocele but 4 showed no improvement with medical treatment; they were submitted to successful probing in the first months of life under general anaesthesia. Nasal endoscopy revealed a nasolacrimal cyst in one patient. True dacryocystocele is relatively rare: ultrasound is a simple, non-invasive method that can reliably distinguish dacryocystocele from other pathological conditions. Several reports have described a variable natural course of these lesions but there are controversial opinions regarding their management. Initially, we treated this congenital anomaly with digital massage, and topical and systemic antibiotics. Probing under general anaesthesia was performed in the event of dacryocystitis or lack of resolution after a short trial period with digital massage. Particular attention was paid to nasal bilateral endoscopy to exclude a nasal obstruction caused by cystic swelling of the nasolacrimal duct. When performed, the probing procedure was successful in all patients.

Two anomalous localizations of mucocele: clinical presentation and retrospective review.

Two Caucasian males (57 and 70 years old) were referred to our attention with parasinus mucoceles, maxillary and frontal mucocele, respectively, that had eroded the orbital rim and caused swelling of the eyelids and brow. Invasion of the orbital space caused several ophthalmic symptoms such as diplopia, proptosis, ptosis, and the formation of a palpable mass. Ophthalmic involvement was the first sign of the mucocele. The mucoceles were completely excised through a skin incision and the diseased mucosa of the sinuses was removed: endonasal fibre optic surgery and the Caldwell-Luc procedure were used in the patient with maxillary mucocele. The cases are described with retrospective review.

Grisel's syndrome: a rare complication following adenoidectomy.

Grisel's syndrome, defined as subluxation of the atlanto-axial joint, not associated with trauma or bone disease, is found primarily in children. There are few references to this syndrome in the ENT literature but it may occur in association with any condition that results in hyperaemia and pathological relaxation of the transverse ligament of the atlanto-axial joint. Several common otolaryngeal conditions have been associated with the syndrome: pharyngitis, adenotonsillitis, tonsillar abscess, cervical abscess, and otitis media. Moreover, the syndrome has been observed after numerous otolaryngologic procedures such as tonsillectomy, adenoidectomy and mastoidectomy. Non-traumatic subluxation of the atlanto-axial joint should be suspected in cases of persistent neck pain and stiffness. X-rays and computed tomography scans of the cervical spine can confirm the diagnosis. Early management, consisting of cervical immobilization and medical treatment, is considered the key factor for a satisfactory outcome. Inappropriate treatment may result in a permanent and painful neck deformity that may even require surgical fusion. Neurological complications have been reported in the literature, with outcome ranging from mild paresthesia, clonus, to quadriplegia or acute respiratory failure and death. The case is described of an 8-year-old boy who developed Grisel's syndrome following adenoidectomy. The pathogenesis, classification, diagnosis, and treatment of this condition are discussed.

Prognostic relevance of cell proliferation in major salivary gland carcinomas.

Several proliferation markers, such as DNA ploidy, Ki67, MiB1 and proliferating cell nuclear antigen have been shown to correlate with clinical course and prognosis in several epithelial tumours and lymphomas. In the present study, the prognostic relevance of these markers was evaluated in major salivary gland carcinomas. A sample of 36 cases out of 85 patients submitted to surgery for major salivary gland carcinomas at our institution between 1987 and 1997 were studied. The sample comprised 8 adenoid-cystic carcinomas, 6 ductal carcinomas, 11 mucoepidermoid carcinomas and 11 acinic cell carcinomas. Follow-up ranged from 1 to 12 years (mean 6.2). In some patients, DNA ploidy (euploid or aneuploid) was studied by flow cytometry. In others, proliferation activity was studied by means of monoclonal antibody MiB1, identifying cells in the proliferative cycle. In some patients, both techniques were used. Follow-up was related to these indices, TNM and stage. Even if ploidy suggested a favourable outcome in diploid cancer (13 favourable vs. 2 unfavourable) and poor outcome in aneuploid cancer (4 favourable vs. 5 unfavourable), the difference was not statistically significant with p = 0.06 in Fisher's exact test. Instead, the proliferative tumour cell fraction, evaluated by MiB1, was statistically correlated with prognosis. Comparing survival curves by Log rank Test it yielded p = 0.007 using an MiB1 cut-off of 5. Applying a cut-off of 20 yielded p = 0.001. Of particular interest were MiB1 values in acinic cell carcinomas for which grading is challenging and lacks consensus. In our group of acinic cell carcinomas, survival correlated with values of MiB1 > or < 15 with p = 0.009 in Log rank test. In conclusion, despite a trend towards correlation between ploidy and prognosis, the present study yielded p = 0.06, whereas the proliferative fraction assessed by MiB1 was significantly correlated with outcomes. Indeed, "growth fraction" in acinic cell carcinomas may stratify different classes of risk.

Schwannoma of cervical sympathetic chain: assessment and management.

Schwannoma arising from the cervical sympathetic chain is an uncommon benign nerve tumour. This tumour most often presents as an asymptomatic solitary neck mass, with slow-growing and rare malignant degeneration. Definitive pre-operative diagnosis may be difficult and investigations are not usually helpful. The carotid artery and internal jugular vein may be displaced anterior-laterally. Diagnosis relies on clinical suspicion and confirmation is often obtained by means of surgical pathology. Surgical excision is the treatment of choice for this tumour, with recurrence being rare. Homer's syndrome is a common post-operative neurological consequence, but does not appear to cause problems to the patient. The case is described of a 42-year-old male who presented an asymptomatic left neck mass. Diagnostic studies included computed tomography, magnetic resonance imaging, and ultrasound which confirmed a circumscribed mass in the upper left portion of the neck next to the thyroid gland. The mass was excised through a transverse left cervical skin incision. Post-operatively the patient showed clinical findings of Horner's syndrome. The pathologic and radiological evaluations, treatment and postoperative complications of this neoplasm are discussed.

[Use of adhesives in emergency surgery]. / L'uso dei collanti in chirurgia d'urgenza.

In a prospective study, the Authors present an analysis on the use of surgical adhesives in the wounds treatment. In sixteen months we have treated 157 patients exclusively with a surgical tissue adhesive 2-octylcianoacrylate to repair traumatic wounds and surgical ones. In the Emergency Department were treated 110 patients (70%) with 2-octylcianoacrylate for skin incisions, lacerations and the length of lesion. We have paid attention to prepare regular wound edges, irrigation and debridement when appropriate to reduce skin tension at the site of laceration. Forty-seven patients (30%) whit surgical skin incisions for thyroidectomy, appendicectomy, hernio-plastic and safenectomy were treated with 2-octyl-cianoacrylate. In both groups of patients, the surgical adhesive has made possible a simple and quick wounds repair as well as good aesthetic results. No relevant complications have been arisen. The writers recommend the surgical adhesive in Emergency Department to abridge waiting time and to avoid the psychological impact caused by local anaesthesia, suture and medications especially in the treatment of all wounds types in children.

[Spontaneous biliodigestive fistulae. The clinical considerations, surgical treatment and complications]. / Fistole bilio-digestive spontanee. Considerazioni cliniche, trattamento chirurgico e complicanze.

To reevaluate the current feature of spontaneous bilioenteric fistula we reviewed 81 cases who had been treated for biliary fistula between 1948 and 1998. After a review of the literature on this subject, the multiple problems relate to pathological anatomy, pathogenesis and physiopathology are discussed. Of 81 patients, 55 were women and 26 were men with the average age of 54.5 years. The most common type of fistula was cholecysto-duodenal (55 cases--68%), followed by cholecysto-colonic (11 cases--13.6%), choledocho-duodenal (7 cases--8.6%), cholecysto-gastric (4 cases--4.9%) and duodeno-left hepatic duct fistula (4 cases). The authors have found in 41 cases the gallstone ileus complications, in 12 cases inflammatory disease of biliary three, in 8 cases hemobilia, gallstone ileus with perforation and digestive hemorrhage compliances respectively. All the patients were treated with surgery. A first procedure consists of enterolithotomy, in gallstone ileus cases, followed by biliary surgery. In 14 patient the general or local conditions argued against one-stage procedure and two-stage procedure had been considered. In 63 patients a cholecystectomy was done, 15 were treated with enterolithotomy and 8 with intestinal resection. Seven patients with gastroduodenal ulcer based fistula have required a gastroduodenal resection. The mortality was 13.6% (11 cases).

[Deep venous thrombosis and neoplastic pathology: our experience in emergencies]. / Trombosi venose profonde e patologia neoplastica: nostro contributo in urgenza.

Deep vein thrombosis incidence is 1/1000 per year; it is associated with many risk factors which is considered as "thrombophilic states". Its pathogenesis is complex, caused by alterations of hemostasis system. Many studies have established the relation between cancer and subsequent venous thromboembolism, confirming the relationship of neoplastic cell interaction with coagulation system. Forty-seven patients admitted to the hospital from 1987 to 1996 with symptomatic clinically proved deep vein thrombosis were included in a retrospective study. Routine examination at the time of diagnosis of deep vein thrombosis revealed an occult cancer in 8 out of 47 patients; 9 out of 47 patients were admitted in hospital with vein thrombosis and known cancer. The aim of this study is to suggest the best, first treatment of vein thromboembolism in emergency to avoid the dangerous pulmonary embolism complication. The patients affected with deep vein thrombosis and cancer were elderly (over 70 years old, in mean); the neoplasia was of digestive system (8/17) in advanced metastatic stage there was cancer familiarity in 7 out of 47 patients. The high risk of pulmonary embolism associated to deep vein thrombosis suggests the importance of early starting the anticoagulant therapy and placing caval filter.

[Echo-color Doppler and echo-Doppler in the diagnosis of carotid body tumors]. / L'eco-color Doppler e l'eco-Doppler nella diagnosi dei chemodectomi latero-cervicali.

Echo-Doppler and Color Flow Doppler examinations, are able to combine the advantages offered by echography with those had with the Doppler exam. In the presence of tumours of the carotid body, these exams can furnish morphological data with regard to tumor size, its precise location and its rapport with contiguous organ as well as data regarding blood flow in the mass itself. The color Flow Doppler exam, in particular, can reveal the echographic aspect and the flow toward and away from the sonde all on the same image. This enables a precise diagnosis of a tumor of the carotid body to be reached even without angiography. The personal experience here reported involves ten cases observed during the last seven years.

5-fluorouracil + folinic acid with cisplatinum and bleomycin in the treatment of advanced head and neck squamous cell carcinoma.

Thirty-six patients with advanced squamous cell carcinoma of the head and neck (SCCHN) were treated with a regimen including cisplatinum (CP) 30 mg/m2 i.v., 5-fluorouracil (5-FU) 500 mg/m2 i.v. bolus, folinic acid (FA) 200 mg/m2 i.v. in a continuous one-hour infusion, and bleomycin (B) 15 mg i.m. on the first and second days and repeated every 28 days. Thirty-three patients (25 with recurrent disease and 8 untreated) are evaluable for objective response. Of these, 4 (12%) achieved CR and 15 (45%) PR. All of the untreated patients responded. The mean duration of response in the patients with recurrent or metastatic disease was 5.5 months (range 2-10+). Remission of symptoms, such as pain and dysphagia, was obtained in 58% and in 44%, respectively. Subjective remission occurred almost exclusively in objectively responsive patients. The major side effects were leukopenia (55%) and nausea/vomiting (58%). This regimen is active in the treatment of advanced SCCHN. The quality of life may be improved in responsive patients.

[Electrophysiologic monitoring of the facial nerve during otoneurosurgery]. / Monitoraggio elettrofisiologico del nervo facciale durante interventi di otoneurochirurgia.

The use of intraoperative facial electromyography (EMG) during otoneurosurgery facilitates anatomic and functional preservation of the VII nerve recording neural activation evoked both mechanically and electrically. The present work presents a personal experience involving the use of this technique in 27 cases of otoneurosurgery (16 neuromas of the acoustic nerve, 4 tympano-jugular paragangliomas, 5 VII nerve decompressions, 1 vestibular neurectomy, and 1 VII nerve neuroma monitored intraoperatively with Nicolet Nerve Integrity Monitor-1 (NIM-2). The latter is a highly sensitive instrument for intraoperative electromyographic recording. It is equipped with a system for electric stimulation, a display and a speaker for the EMG signal and acoustic alarm. During monitoring basically 3 types of EMG responses can be recorded: "burst", "train" and "pulse". In the present work the various EMG patterns are analyzed in detail as well as the relationship between their emergence and the type of surgical procedure performed. Intraoperative interpretation of the EMG activity makes possible more precise, intricate surgical maneuvers. It is felt that intraoperative monitoring has made it possible to preserve the anatomy and functionality of the facial nerve more frequently than is possible with other unmonitored cases. This becomes most evident when evaluating the long-term results.

Does breast feeding protect against the development of clinical symptoms of celiac disease in children?

A retrospective approach has been adopted to investigate the frequency and duration of breast feeding and the time of gluten introduction in the diet in 216 celiac children and their healthy siblings of three different centers--Naples, Milan, and Turin. In this matched case-control study, the selected controls were healthy siblings of the cases. Children formula-fed from birth, or breast-fed for less than 30 days, were found to have a relative risk of developing symptoms of celiac disease four times higher than children breast-fed for more than 30 days (p less than 0.0001). To investigate more deeply the effect of the duration of breast feeding as a possible protecting factor, the linear trend for different periods of breast feeding was tested and found to be highly significant (G1: 18.3 with 1 df). Therefore, increased duration of breast feeding is associated with decreased risk of developing celiac symptoms. On the contrary, there was no apparent relationship between early introduction of gluten into the diet and frequency of celiac disease. Our findings are consistent with the hypothesis that a wider diffusion of breast feeding is a factor underlying the recently reported decrease of the incidence of celiac disease in children.