Fragmentomic analysis of circulating tumor DNA-targeted cancer panels

BACKGROUND

The isolation of cell-free DNA (cfDNA) from the bloodstream can be used to detect and analyze somatic alterations in circulating tumor DNA (ctDNA), and multiple cfDNA-targeted sequencing panels are now commercially available for Food and Drug Administration (FDA)-approved biomarker indications to guide treatment. More recently, cfDNA fragmentation patterns have emerged as a tool to infer epigenomic and transcriptomic information. However, most of these analyses used whole-genome sequencing, which is insufficient to identify FDA-approved biomarker indications in a cost-effective manner.

PATIENTS AND METHODS

We used machine learning models of fragmentation patterns at the first coding exon in standard targeted cancer gene cfDNA sequencing panels to distinguish between cancer and non-cancer patients, as well as the specific tumor type and subtype. We assessed this approach in two independent cohorts: a published cohort from GRAIL (breast, lung, and prostate cancers, non-cancer, n = 198) and an institutional cohort from the University of Wisconsin (UW; breast, lung, prostate, bladder cancers, n = 320). Each cohort was split 70%/30% into training and validation sets.

RESULTS

In the UW cohort, training cross-validated accuracy was 82.1%, and accuracy in the independent validation cohort was 86.6% despite a median ctDNA fraction of only 0.06. In the GRAIL cohort, to assess how this approach performs in very low ctDNA fractions, training and independent validation were split based on ctDNA fraction. Training cross-validated accuracy was 80.6%, and accuracy in the independent validation cohort was 76.3%. In the validation cohort where the ctDNA fractions were all <0.05 and as low as 0.0003, the cancer versus non-cancer area under the curve was 0.99.

CONCLUSIONS

To our knowledge, this is the first study to demonstrate that sequencing from targeted cfDNA panels can be utilized to analyze fragmentation patterns to classify cancer types, dramatically expanding the potential capabilities of existing clinically used panels at minimal additional cost.

Sixty-six cases of intrauterine fetal death. A prospective study with an extensive test protocol

BACKGROUND

A prospective study was performed to elucidate the etiology of intrauterine fetal death and to evaluate diagnostic procedures.

METHODS

Sixty-six stillbirth cases with a gestational age of more than 25 complete weeks were studied, using an extensive test protocol. The validity of the cause of death was classified as certain, probable, possible and unexplained. The extent to which the diagnostic measures had been performed was classified: patients in whom none or only a few tests were performed, patients partially tested and patients completely tested.

RESULTS

The cause of death was certain in 57%, probable in 20%, and possible in 11% of the cases. In only 12% of the cases did the cause of death remain entirely unexplained. The principal causes of IUFD were infections, including premature rupture of the membranes (15%), anomalies (11%), preeclampsia-associated conditions (9%) and intrauterine growth retardation of unknown etiology (8%). In this series, less well-known conditions, such as circulating maternal autoantibodies and feto-maternal transfusion, also appeared to play an important role in causing intra-uterine fetal death.

CONCLUSIONS

An extensive and relevant test protocol provides information as to the cause of death in the majority of cases. Future protocols should include tests for autoimmune antibodies and feto-maternal transfusion.

Allo-immunization during pregnancy. Clinical results from 1983 to 1989 in a Scandinavian university hospital

From 1983 to 1989, 147,068 pregnancies were analyzed for allo-immunization against erythrocyte antigens. Approximately half of the cases were due to immunization against factor D and the others were due to allo-immunization against other antigens (K, c, E, etc.). In 61 cases exchange transfusion of the newborn was needed and in 115 cases diagnostic amniocentesis was done during pregnancy. Intrauterine transfusions were performed in 10 cases. Fetal and neonatal mortality was 4% in these moderate to severe cases, all due to immunization against D. Immunization against D was due to failure to give immunoglobulin anti-D in about 2/3 of the cases. Systematic prophylactic treatment with anti-D during pregnancy would probably not be cost-effective in this population.

Accelerated intracranial occlusive disease, oral contraceptives, and cigarette use

We report clinical and angiographic features of accelerated intracranial occlusive disease resembling moyamoya vasculopathy in five young women who used oral contraceptives (OCs) and smoked cigarettes, but generally had no other obvious risk factors for cerebrovascular disease. Three women had been on OCs for at least 4 years, one woman each had been on OCs for 3 months and for 2 weeks. All five women had smoked cigarettes for at least eight pack-years. Intermittent and progressive multifocal cognitive, visual, motor, or sensory hemispheric symptoms and signs developed in all. All patients developed strokes, four preceded by transient ischemic attacks. Cerebral angiography demonstrated bilateral supraclinoid internal carotid artery stenosis in four patients and proximal posterior cerebral artery stenosis in one. Additional features included rete mirabile, telangiectasias, prominent lenticulostriate collaterals, and multifocal distal cerebral branch occlusions. Three had mild abnormalities of serum fibrinogen, antinuclear antibody, erythrocyte sedimentation rate, or CSF IgG. After discontinuing OCs and reducing cigarette use, four women have not had further strokes over a mean follow-up of approximately 5 years. In certain young women, clinical and angiographic features resembling moyamoya may develop with the use of OCs and cigarettes. We speculate that an immunologically mediated vasculopathy may explain, in part, this unusual cerebrovascular syndrome in otherwise healthy young women.

Diabetic truncal neuropathy presenting as abdominal hernia

Two patients with longstanding type II diabetes mellitus presented with focal, unilateral protrusion of the abdominal wall, thought to be due to abdominal hernia. They were evaluated extensively for intra-abdominal pathology but none was found. In one patient, the protrusion was associated with spontaneous burning pain and hyperpathia, but in the other it was painless. In the patient seen during the acute phase there was denervation in paraspinal and abdominal muscles on EMG examination. In both patients, the protrusion subsided without specific treatment in 2 to 4 months. This seldom-described manifestation of diabetic truncal neuropathy masquerading as abdominal hernia needs a higher profile to avoid misdiagnosis and unnecessary investigation. Diagnosis may be quickly established by EMG examination of the paraspinal and abdominal muscles.

Visual symptoms associated with the presence of a lupus anticoagulant

The lupus anticoagulant is an acquired serum immunoglobulin that prolongs several coagulation parameters, most notably the partial thromboplastin time (PTT). Most commonly, this condition is found in association with systemic lupus erythematosus (SLE) but may be seen with other collagen-vascular diseases and in otherwise healthy individuals. Despite the laboratory tests suggesting impaired coagulation, clinically the lupus anticoagulant has been associated with thrombosis. The authors present five patients with the lupus anticoagulant who came to medical attention because of branch retinal artery occlusion, ischemic optic neuropathy, transient visual loss, transient diplopia, or vertebrobasilar insufficiency. Eleven previously reported patients with the lupus anticoagulant and disturbed vision are also reviewed with additional findings of retinal venous occlusive disease and homonymous visual field loss. The relationship of these findings to retinopathy in SLE is discussed. Patients with the lupus anticoagulant (with or without SLE) may develop disturbances in vision due to thrombosis from a hypercoagulable state. We recommended obtaining a PTT, VDRL, and the more sensitive anticardiolipin antibody in patients with unexplained visual symptoms.

Influence of the pelvic outlet capacity on fetal head presentation at delivery

The influence of pelvic outlet capacity on fetal head presentation in 1,402 term primiparas with normal pregnancies was studied. In all cases radiological pelvimetry was carried out and labor started spontaneously. Occiput posterior (OP) delivery occurred in 5.1%. As pelvic outlet capacity decreased an increased frequency of OP presentations and need for epidural anesthesia (EDA) was found. With OP presentation the duration of labour was longer, the frequency of EDA, instrumental delivery, cesarean section and low Apgar score at 1 minute were all higher, all compared with occiput anterior (OA) presentation. No difference in fetal morbidity was found. When the influence of the pelvic outlet capacity was eliminated through comparison of matched groups, the course of delivery became more similar whether the presentation was OA or OP and the frequency of EDA became the same. Reduced pelvic outlet capacity seemed to be one cause of both OP presentation and the use of EDA.

Influence of pelvic outlet capacity on labor. A prospective pelvimetry study of 1,429 unselected primiparas

The influence of pelvic outlet capacity on labor and the efficiency of routine low-dose radiological pelvimetry to anticipate dystocia during labor were studied prospectively among 1,429 unselected term primiparas, all having fetal head presentation and normal pregnancy. Outlet contraction was found in 0.9% and borderline outlet measurement in 5.3%. In 1,402 cases labor started spontaneously and 83 emergency cesarean sections were done. The incidence of cesarean section because of dystocia increased in inverse proportion to decreasing pelvic outlet capacity. The incidence of other emergency cesarean sections was not influenced by pelvic outlet size. In 79% of cesarean section interventions due to dystocia, pelvic outlet capacity was normal. Apgar score less than 7 at one minute was more commonly associated with a small pelvic outlet. Apgar score at 5 minutes and neonatal morbidity were not influenced by pelvic outlet size. Pelvic outlet capacity had a marked influence on the mode of delivery, but the practical value of radiological pelvimetry by fetal head presentation is rarely considered, except in very selected cases.

The pelvic outlet. A comparison between clinical evaluation and radiologic pelvimetry

A random sample of 798 primiparas was screened with clinical evaluation and radiologic low-dose pelvimetry of the pelvic outlet. The purpose was to study the accuracy of clinical evaluation in comparison with X-ray pelvimetry and to determine whether clinical evaluation could reveal any other factor influencing labor. A significant agreement between clinical and X-ray pelvimetry was found, but the sensitivity of clinical evaluation was low and as many as half the patients with a contracted pelvis, according to pelvimetry, were not detected. Delivery outcomes in two matched groups with similar pelvic outlet measurements but different clinical evaluation did not differ, indicating that clinical evaluation did not detect any other factor not revealed by X-ray pelvimetry.

Bioconversion of arachidonic acid in human pregnant uterine cervix

The in vitro conversion of [14C]arachidonic acid by endocervical mucosa and cervical tissue specimens obtained in first trimester (9-12 w) and term pregnant patients (37-39 w) was studied in whole-cell homogenates. All radiolabelled products of the arachidonic acid cascade were extracted, purified and separated utilizing silicic acid chromatography, thin-layer chromatography and reversed phase partition chromatography and identified with radio-gas chromatography and gas chromatography-mass spectometry. Both types of tissue produced PGF2 alpha and PGE2, as well as TxB2. In cervical tissue specimens there was a significant increase in the production of all these three prostaglandins as the pregnancy progressed, whereas no such difference was seen in homogenates of endocervical mucosa. In both endocervical mucosa and cervical tissue specimens there was a highly significant increase in the production of a so-far unknown compound(s), in samples from term patients as compared with samples from first-trimester patients. The possible participation of this metabolite of [14C]arachidonic acid in the regulation of cervical ripening is discussed.

Postpartum perforation of the colon due to endometriosis

A case is reported of a ruptured endometriotic lesion following childbirth. Immediately after her second delivery, the 34-year-old parturient developed acute abdominal pain. At operation a ruptured left-sided ovarian abscess with a fistula to the colon was found. Endometriosis was present in the ovarian wall and the adjacent colon. Endometriosis as a cause of acute abdominal pain during pregnancy should be kept in mind.

Experience with an industrially manufactured gel PGE2 for cervical priming

An industrially manufactured ready-to-use PGE2 gel for cervical ripening was clinically evaluated. The study included 42 primiparous and eight multiparous women with an unfavourable cervix (Bishop score less than or equal to 5) admitted to hospital for induction of labour on medical grounds. PGE2, 0.5 mg, in 2 ml triacetin gel was instilled into the cervical canal. In nine patients (18%) the gel induced labour and subsequent delivery. In the remaining women the mean Bishop score increased from 3.0 to 7.7 during a 24-h period and labour was induced by either i.v. oxytocin or PGF2 alpha. None of the 50 patients experienced gastrointestinal side effects during pretreatment with PGE2. In 50% of the patients slight uterine contractility was noticed. All patients went into labour. The incidence of Cesarean section was 10%. Except for two patients treated because of intrauterine fetal death there was no perinatal mortality. The 5-min Apgar score was 8 or more in all newborn but 1. The main advantage of the new gel is that it is ready to use without any mixing procedure. Moreover, the stability of PGE2 is sufficient to allow routine clinical use.

Obstetrical paracervical block with chloroprocaine or bupivacaine. A comparison

Obstetrical paracervical block was randomly administered to 47 patients, using either 2% chloroprocaine or 0.25% bupivacaine. Analgesia and onset of analgesia were similar for both drugs, but the duration of chloroprocaine was only about half that of bupivacaine (35 min versus 66 min). Fetal bradycardia was encountered in one case after chloroprocaine and in two cases after bupivacaine. It is concluded that chloroprocaine plain is not very suitable for obstetrical paracervical block due to its short duration of action.