Abstract: A method of identifying methylated cell-free DNA (cfDNA) biomarkers is provided, referred to as layered analysis of methylated biomarkers (LAMB). In particular, the LAMB methodology can be used to analyze data from patients to discover methylated cfDNA biomarkers associated with cancer. LAMB was used to identify tumor suppressor candidates using meta-analysis of cancer tissue methylation studies, followed by screening for tumor-specific promoter CpGs in these tumor suppressors and analysis of microarray data for cancerous tissues, non-cancerous tissues adjacent to tumors, and healthy blood samples. Biomarker panels for diagnosis of liver, colorectal, prostate, and lung cancer as well as biomarkers for predicting tumor response to therapy are provided based on this LAMB methodology. The biomarkers identified by LAMB can be used alone or in combination with one or more additional biomarkers or relevant clinical parameters in prognosis, diagnosis, therapy selection, or monitoring treatment of cancer.

Abstract: A medical device for retrieval of kidney stone fragments from a urinary tract is provided. The medical device has a plurality of magnets arranged within a flexible sheath forming a flexible wire. The magnets are magnetically attached end-to-end and arranged with their magnetic polarities alternating in direction. The magnetization direction of each of the magnets is orthogonal to the length axis of the flexible wire. A removable inner stylet is situated within the flexible sheath allowing for modifiable flexibility of the wire. The medical device is dimensioned to be introduced into the urinary tract and standard endoscopic devices. The medical device is further dimensioned to allow for the wire with magnetically attached stone fragments to be retrieved from the urinary tract. The magnetic field along the length axis is sufficient to attract to the surface of the flexible wire superparamagnetic nanoparticles which have bound themselves to kidney stone fragments.

Abstract: Compositions, methods, and kits are provided for diagnosing hepatocellular carcinoma in patients. In particular, methylated cell-free DNA biomarkers and methods of using them to determine if a patient has hepatocellular carcinoma are provided. Additionally, the methylated cell-free DNA biomarkers can be used to distinguish between patients with a chronic liver disease such as cirrhosis who do not have hepatocellular carcinoma and those patients with a chronic liver disease who have hepatocellular carcinoma. The identified biomarkers can be used alone or in combination with one or more additional biomarkers or relevant clinical parameters in prognosis, diagnosis, therapy selection, or monitoring treatment of hepatocellular carcinoma.

Abstract: Compositions, methods, and kits are provided for diagnosing and treating prostate cancer. In particular, cell-free DNA biomarkers have been identified that can be used to aid in diagnosis, selection of treatment, and monitoring of treatment of prostate cancer.

Abstract: This work provides a method and device for performing quantitative and sensitive multiplex nucleic acid detection at the point-of-care using magnetoresistive (MR) detection. Temperature calibration of the MR sensor elements is performed per-element, rather than assuming the same calibration parameters apply to each element of the MR sensor array. It can include a digitally controlled fluidic system to allow automated wash and reagent injection, an on-chip temperature management system to achieve on-chip polymerase chain reactions (PCR), and a portable magnetoresistive sensor platform. This approach requires minimal user involvement beyond adding the sample and simple top-level control, making it highly desirable for point-of-care applications.

Abstract: A medical device for retrieval of kidney stone fragments from a urinary tract is provided. The medical device has a plurality of magnets arranged within a flexible sheath forming a flexible wire. The magnets are magnetically attached end-to-end and arranged with their magnetic polarities alternating in direction. The magnetization direction of each of the magnets is orthogonal to the length axis of the flexible wire. A removable inner stylet is situated within the flexible sheath allowing for modifiable flexibility of the wire. The medical device is dimensioned to be introduced into the urinary tract and standard endoscopic devices. The medical device is further dimensioned to allow for the wire with magnetically attached stone fragments to be retrieved from the urinary tract. The magnetic field along the length axis is sufficient to attract to the surface of the flexible wire superparamagnetic nanoparticles which have bound themselves to kidney stone fragments.

Abstract: Improved temperature measurement and correction is provided for magnetoresistive sensor arrays. A linear coefficient of resistance vs. temperature is determined from one or more reference sensors in the array by measuring resistance of the reference sensors at known temperatures, which enables resistance measurements to be used to determine unknown temperatures in all sensors of the array. Double modulation leads to MR sensor outputs having center tones which can be used to correct temperature dependence in side tone MR signals. This correction can be according to a linear fit or a polynomial fit. Applications include biological assays requiring accurate temperature data, such as accurate determination of DNA melting curves.

Abstract: Small molecule analytes (less than 1000 Daltons) in a fluid sample are detected using a competitive assay in a magnetic biosensor. The fluid sample is added to a biosensor detection chamber together with detection probes and magnetic tags which bind to the detection probes. The magnetic biosensor is functionalized with a capture probe that shares an epitope with the analytes, and the detection probe is capable of binding the epitope shared by the analytes and the capture probe, so that the presence of the analyte prevents detection probes (and magnetic tags) from binding to the biosensor. By measuring the binding of the magnetic tags to the magnetic biosensor, an amount of analytes in the solution is determined.

Abstract: Small molecule analytes (less than 1000 Daltons) in a fluid sample are detected using a competitive assay in a magnetic biosensor. The fluid sample is added to a biosensor detection chamber together with detection probes and magnetic tags which bind to the detection probes. The magnetic biosensor is functionalized with a capture probe that shares an epitope with the analytes, and the detection probe is capable of binding the epitope shared by the analytes and the capture probe, so that the presence of the analyte prevents detection probes (and magnetic tags) from binding to the biosensor. By measuring the binding of the magnetic tags to the magnetic biosensor, an amount of analytes in the solution is determined.

Abstract: An integrated microfluidic biochip is provided that includes a microfluidic device, where the microfluidic device includes hollow structures, where at least one the hollow structure includes an output at a bottom surface of the microfluidic device, and a sensor plate, where the sensor plate comprises a plurality of independent surface sensors, where the microfluidic device is sealably attachable to the sensor plate, where the hollow structure output abuts the surface sensor when the microfluidic device is attached to the sensor plate.

Abstract: A method for identification of circulating tumor cells (CTCs) in a blood sample uses magnetic enrichment and a nanowell assay. The CTCs are magnetically labeled with cancer cell markers conjugated to magnetic nanoparticles and then separated by passing the blood sample through a magnetic sifter. The enriched CTCs are then loaded into a microfluidic single-cell molecular assay comprising an array of 25,600 or more nanowells, each containing at most a single one of the CTCs. Using multiple fluorescent gene markers, simultaneous multiple-color multiplexed gene expression of the CTCs is performed, preferably using RT-PCR. Images of fluorescence signals from individual nanowells are analyzed to identify CTCs.

Abstract: Correlated double sampling (CDS) for magnetoresistive (MR) sensors is provided. Here the MR sensor output is sampled at two closely spaced times. The first sample is MR signal+baseline+noise and is sampled when the modulated magnetic field is non-zero. The second sample is baseline+noise only because it is sampled when the modulated magnetic field is zero. The difference between the first and second samples will have significantly reduced low frequency noise and baseline cancellation. Modulation of the electrical bias provided to the MR sensor can be used to provide a baseline signal for temperature compensation. In a second aspect, we provide MR sensor arrays having input and output multiplexing and demultiplexing for row and column line selection, in combination with a per-sensor switch to prevent noise accumulation and bandwidth reduction from idle MR sensors.

Abstract: Improved temperature measurement and correction is provided for magnetoresistive sensor arrays. A linear coefficient of resistance vs. temperature is determined from one or more reference sensors in the array by measuring resistance of the reference sensors at known temperatures, which enables resistance measurements to be used to determine unknown temperatures in all sensors of the array. Double modulation leads to MR sensor outputs having center tones which can be used to correct temperature dependence in side tone MR signals. This correction can be according to a linear fit or a polynomial fit. Applications include biological assays requiring accurate temperature data, such as accurate determination of DNA melting curves.

Abstract: A method of methylation detection provides a quantitative description of the methylation density in DNA strands. Bisulphite conversion [100] of the DNA strands containing methylated and unmethylated sites creates converted DNA strands with mismatch base pairs. The converted DNA strands are PCR amplified [102], and single strand target DNA strands are magnetically labeled [104] and hybridized [106] with complementary DNA strands immobilized onto a magnetoresistive (MR) sensor array. During hybridization, a binding signal may be recorded. A stringency condition such as temperature or salt concentration is increased [108] to cause the magnetically labeled single strand target DNA strands to be denatured from the complementary DNA strands immobilized onto a magnetoresistive (MR) sensor array.

Abstract: Methods for quantitatively determining a binding kinetic parameter of a molecular binding interaction are provided. Aspects of embodiments of the methods include: producing a magnetic sensor device including a magnetic sensor in contact with an assay mixture including a magnetically labeled molecule to produce a detectable molecular binding interaction; obtaining a real-time signal from the magnetic sensor; and quantitatively determining a binding kinetics parameter of the molecular binding interaction from the real-time signal. Also provided are systems and kits configured for use in the methods.

Abstract: Correlated double sampling (CDS) for magnetoresistive (MR) sensors is provided. Here the MR sensor output is sampled at two closely spaced times. The first sample is MR signal+baseline+noise and is sampled when the modulated magnetic field is non-zero. The second sample is baseline+noise only because it is sampled when the modulated magnetic field is zero. The difference between the first and second samples will have significantly reduced low frequency noise and baseline cancellation. Modulation of the electrical bias provided to the MR sensor can be used to provide a baseline signal for temperature compensation. In a second aspect, we provide MR sensor arrays having input and output multiplexing and demultiplexing for row and column line selection, in combination with a per-sensor switch to prevent noise accumulation and bandwidth reduction from idle MR sensors.

Abstract: Correlated double sampling (CDS) for magnetoresistive (MR) sensors is provided. Here the MR sensor output is sampled at two closely spaced times. The first sample is MR signal+baseline+noise and is sampled when the modulated magnetic field is non-zero. The second sample is baseline+noise only because it is sampled when the modulated magnetic field is zero. The difference between the first and second samples will have significantly reduced low frequency noise and baseline cancellation. Modulation of the electrical bias provided to the MR sensor can be used to provide a baseline signal for temperature compensation. In a second aspect, we provide MR sensor arrays having input and output multiplexing and demultiplexing for row and column line selection, in combination with a per-sensor switch to prevent noise accumulation and bandwidth reduction from idle MR sensors.

Abstract: Methods for analyte detection with magnetic sensors are provided. Aspects of the methods include producing a magnetic sensor device having a magnetically labeled analyte from a sample, such as a serum sample, bound to a surface of a magnetic sensor thereof; and obtaining a signal, e.g., a real-time signal, from the magnetic sensor to determine whether the analyte is present in the sample. Also provided are devices, systems and kits that find use in practicing the methods of the invention. The methods, devices, systems and kits of the invention find use in a variety of different applications, including detection of biomarkers, such as disease markers.

Abstract: A method for identification of circulating tumor cells (CTCs) in a blood sample uses magnetic enrichment and a nanowell assay. The CTCs are magnetically labeled with cancer cell markers conjugated to magnetic nanoparticles and then separated by passing the blood sample through a magnetic sifter. The enriched CTCs are then loaded into a microfluidic single-cell molecular assay comprising an array of 25,600 or more nanowells, each containing at most a single one of the CTCs. Using multiple fluorescent gene markers, simultaneous multiple-color multiplexed gene expression of the CTCs is performed, preferably using RT-PCR. Images of fluorescence signals from individual nanowells are analyzed to identify CTCs.

Abstract: A method of fabricating in-plane or out-of-plane thin-film multi-axial magnetic anisotropy devices is provided that includes either depositing a magnetic material with perpendicular or partially perpendicular anisotropy patterned into a multi-directional, curved, or closed path or depositing a thin-film of magnetic material on a piezoelectric material, where the magnetic material is arranged in a pattern, depositing excitation electrodes on the piezoelectric material, where the excitation electrodes are arranged in a pattern, biasing the piezoelectric material, by applying a voltage across the excitation electrodes, where an electric field through the piezoelectric material is generated by the applied voltage across the excitation electrodes, where the piezoelectric material is biased by the electric field to provide stress to the magnetic material, where the stress rotates a magnetization of the magnetic material, and patterning the magnetic material into a multi-directional, curved, or closed path.